Biowulf High Performance Computing at the NIH
Scientific Applications on NIH HPC Systems

The NIH HPC staff maintains several hundred scientific programs, packages and databases for our users. Below is a list of system-installed software available on Biowulf and Helix. Click on the application name to get to site-specific instructions on how to run a given package on the cluster, including links to the original application documentation.

In almost all cases, applications are made available through the use of environment modules.

back to top

Acemd (2019-10-02)

ACEMD is a high performance molecular dynamics code for biomolecular systems designed specifically for NVIDIA GPUs. Simple and fast, ACEMD uses very similar commands and input files of NAMD and output files as NAMD or Gromacs.

AMBER (20)

AMBER (Assisted Model Building with Energy Refinement) is a package of molecular simulation programs.

AMPL (1.0.0)

The Accelerating Therapeutics for Opportunites in Medicine (ATOM) Consortium Modeling PipeLine for Drug Discovery. AMPL is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

APBS (1.5)

APBS (Adaptive Poisson-Boltzmann Solver) is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.

Autodock (4.2.6)

Autodock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

AutodockVina (1_1_2)

AutoDock Vina is a program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. It is closely tied to Autodock.

CHARMM (c45b1)

CHARMM is a general and flexible software application for modeling the structure and behavior of molecular systems.

cryoDRGN (0.3.1)

CryoDRGN is an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It contains interactive tools to visualize a dataset’s distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions.

GAMESS (30Jun20-R1)

GAMESS is a general ab initio quantum chemistry package.

Gaussian (G16-C01)

Gaussian is a connected system of programs for performing semiempirical and ab initio molecular orbital (MO) calculations.

Gromacs (2020.2)

Gromacs is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

NAMD (2.14)

NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. VMD, the associated molecular visualization program, is also available.

ORCA (4.2.1)

ORCA is an ab initio, DFT, and semi-empirical SCF-MO package.

Psi4 (1.2)

Psi4 is an ab-initio electronic structure code that supports various methods for calculating energies and gradients of molecular systems.

Q-Chem (5.0.1)

Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra.

Schrodinger (2020.4)

A limited number of Schrödinger applications are available on the Biowulf cluster through the Molecular Modeling Interest Group. Most are available through the Maestro GUI.

VMD (1.9.3)

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. To use, type vmd at the prompt.

back to top

BioBERT (v20200409)

BioBERT is a biomedical language representation model designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.

BioGANs (20191230)

BioGANs is a novel application of Generative Adversarial Networks (GAN) to the synthesis of cells imaged by fluorescence microscopy. It allows to infer the correlation between the spatial pattern of different fluorescent proteins that reflects important biological functions. The synthesized images capture these relationships, which are relevant for biological applications.

CANDLE (main)

Open-source software platform providing highly scalable deep learning methodologies, including intelligent hyperparameter optimization.

The accurate identification of DNA sequence variants is particularly difficult for single molecule sequencing, which has a high per-nucleotide error rate (~5%-15%). Clairvoyante implements a multitask five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. Using well-characterized tesing data, Clairvoyante achieved 99.73%, 97.68% and 95.36% precision on known variants, and 98.65%, 92.57%, 77.89% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively.

cryoDRGN (0.3.1)

CryoDRGN is an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It contains interactive tools to visualize a dataset’s distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions.

cuDNN (8.0.3)

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cuDNN provides highly tuned implementations for standard routines such as forward and backward convolution, pooling, normalization, and activation layers.

DanQ (20191107)

DanQ is a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

DeepHiC (20201001)

DeepHiC ("deep Hi-C") is a generative adversarial network aimed at predicting the high-resolution Hi-C contact maps from ithe low-coverage sequencing data. Hi-C is commonly used to study three-dimensional genome organization.

DeepHit (20201211)

The DeepHit application uses a deep neural network to learn the distribution of survival times directly. DeepHit makes no assumptions about the underlying stochastic process and allows for the possibility that the relationship between covariates and risk(s) changes over time. Most importantly, DeepHit smoothly handles competing risks; i.e. settings in which there is more than one possible event of interest.

DeepLab (20180816)

DeepLab is a Semantic Image Segmentation tool. It makes use of the Deep Convolutional Networks, Dilated (a.k.a. Atrous) Convolution, and Fully Connected Conditional Random Fields.

DeepLabCut (;; 2.2b7)

DeepLabCut is an open source toolbox that builds on a state-of-the-art human pose estimation algorithm. It allows training of a deep neural network by using limited training data to precisely track user-defined features, so that the human labeling accuracy will be matched.

DeepM6A (0.1)

DeepM6A application implements a deep-learning-based algorithm for predicting potential DNA 6mA sites de novo from sequence at single-nucleotide resolution. Application of this tool to three representative model organisms, Arabidopsis thaliana, Drosophila melanogaster and Escherichia coli, demonstrated that it supercedes the conventional k-mer-based approaches in both accuracy and performance.

digits (5.0)

DIGITS simplifies common deep learning tasks such as managing data, designing and training neural networks on multi-GPU systems, monitoring performance in real time with advanced visualizations, and selecting the best performing model from the results browser for deployment. DIGITS is completely interactive so that data scientists can focus on designing and training networks rather than programming and debugging.

genoml (1.0.3)

GenoML is an Automated Machine Learning tool that optimizes machine learning pipelines for genomic data. GenoML will automate the most tedious part of machine learning by intelligently exploring thousands of possible models to find the best one for your data.

meka (1.9.2)

A Multi-label Extension to WEKA

PolyRNN++ (20180718)

Manually labeling datasets with object masks is extremely time consuming. PolyRNN++ produces polygonal annotations of objects interactively using humans-in-the-loop. It employs Convolutional Neural Network encoder trained with Reinforcement Learning.

ReLeaSE (20200516)

ReLeaSE (Reinforcement Learning for Structural Evolution) is an application for de-novo Drug Design based on Reinforcement Learning. It integrates two deep neural networks: generative and predictive, that are trained separately but are used jointly to generate novel targeted chemical libraries. ReLeaSE uses simple representation of molecules by their simplified molecular input line entry specification (SMILES) strings only.

spacy (2.2.3)

advanced Natural Language Processing (NLP) in Python

SpliceAI (1.3)

SpliceAI is a deep neural network that accurately predicts splice junctions from an arbitrary pre-mRNA transcript sequence, enabling precise prediction of noncoding genetic variants that cause cryptic splicing.

tensorrt (18.09)

NVIDIA TensorRT™ is a platform for high-performance deep learning inference. It includes a deep learning inference optimizer and runtime that delivers low latency and high-throughput for deep learning inference applications. TensorRT-based applications perform up to 40x faster than CPU-only platforms during inference. With TensorRT, you can optimize neural network models trained in all major frameworks, calibrate for lower precision with high accuracy, and finally deploy to hyperscale data centers, embedded, or automotive product platforms.

Tybalt (20190214)

Tybalt implements a Variational EutoEncoder (VAE), a deep neural network approach capable of generating meaningful latent spaces for image and text data. Tybalt has been trained on The Cancer Genome Atlas (TCGA) pan-cancer RNA-seq data and used to identify specific patterns in the VAE encoded features.

UNet (20190225)

U-Net is an image segmentation tool. It relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization.

YOLO (20200211)

YOLO is a new approach to object detection. Prior work on object detection repurposed classifiers to perform detection. Instead, YOLO frames object detection as a regression problem to spatially separated bounding boxes and associated class probabilities.

back to top

abruijn (1.0)

ABruijn is a assembler for long reads from, for example, PacBio and Oxford Nanopore Technologies sequencers.

abyss (2.2.4)

Abyss represents Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. The parallel version is implemented using MPI and is capable of assembling larger genomes.

adam (0.25.0)

ADAM is a library and command line tool that enables the use of Apache Spark to parallelize genomic data analysis across cluster/cloud computing environments. ADAM uses a set of schemas to describe genomic sequences, reads, variants/genotypes, and features, and can be used with data in legacy genomic file formats such as SAM/BAM/CRAM, BED/GFF3/GTF, and VCF, as well as data stored in the columnar Apache Parquet format. On a single node, ADAM provides competitive performance to optimized multi-threaded tools, while enabling scale out to clusters with more than a thousand cores. ADAM's APIs can be used from Scala, Java, Python, R, and SQL.

AfterQC (0.9.6)

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.

albacore (2.3.3)

ONT basecaller

angsd (0.932)

ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes.

AnnotSV (2.2)

AnnotSV is a program designed for annotating Structural Variations (SV). This tool compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to i) interpret SV potential pathogenicity and ii) filter out SV potential false positives.

ANNOVAR (2019-10-24)

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes.

ascatNgs (4.5.0)

AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing.

atactk (0.1.6)

A toolkit for working with ATAC-seq data.

atac_dnase_pipelines (0.3.4-19-gcbd2a00)

This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data

atropos (1.1.18)

An NGS read trimming tool that is specific, sensitive, and speedy.

augustus (3.3.3)

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

bam2fastq (1.1.0)

This tool is used to extract raw sequences (with qualities) from bam files.

bam2mpg (1.0.1)

The program “bam2mpg” calls genotypes from sequence reads of haploid or diploid DNA aligned to a closely-related reference sequence. The program reads alignments in BAM format ( The MPG (Most Probable Genotype) algorithm is based on a Bayesian model which simulates sampling from one or two alleles with sequencing error, and then calculates the likelihood of each possible genotype given the observed sequence data.

bamliquidator (1.3.8)

bamliquidator is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format.

bamreadcount (cram-v0.0.1)

Bam-readcount generates metrics at single nucleotide positions. There are number of metrics generated which can be useful for filtering out false positive calls.

BAMSurgeon (1.2)

Tools for adding mutations to existing .bam files; used for testing mutation callers

bamtools (2.5.1)

BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.

bamUtil (1.0.14)

bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

basespace_cli (0.8.12)

Command line interface for Illumina's BaseSpace

bazam (1.0.1)

A tool to extract paired reads in FASTQ format from coordinate sorted BAM files

bbtools (38.87)

An extensive set of bioinformatics tools including bbmap (short read aligner), bbnorm (kmer based normalization), dedupe (deduplication and clustering of unaligned reads), reformat (formatting and trimming reads) and many more.

bcbio-nextgen (1.2.3)

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcl2fastq (2.20)

a tool to handle bcl conversion and demultiplexing

bedops (2.4.39)

Bedops is a suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets - BEDOPS aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

bedtools (2.30.0)

The BEDTools utilities allow one to address common genomics tasks such finding feature overlaps and computing coverage. In addition, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together.

BETA (1.0.7)

Binding and expression target analysis (BETA) is a software package that integrates ChIP-seq of TFs or chromatin regulators with differential gene expression data to infer direct target genes. The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression.

BFC (1.0-7-g69ab176)

BFC is a standalone tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.

bigSCale2 (20190729)

bigSCale is a complete framework for the analysis and visualization of single cell data. It allows to cluster, phenotype, perform pseudotime analysis, infer gene regulatory networks and reduce large datasets in smaller datasets with higher quality.

binlorry (1.3.1)

BinLorry is a tool for binning and filtering sequencing reads into distinct files. Reads can be binned and filtered by any attributes encoded in their headers, documented in a CSV file or by length.

bioawk (1.0)

Regular awk with support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.

biobambam2 (2.0.144)

Tools for early stage alignment file processing.

biom-format (2.1.10)

tool (and library) to manipulate Biological Observation Matrix (BIOM) Format files

bismark (0.23.0)

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.

bison (0.4.0)

BISON is a bisulfite-converted short-read aligner that can natively utilize high-performance computing clusters to increase speed.

bowtie (1.3.0)

bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.

bowtie2 (2.4.2)

A version of bowtie that's particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes

BRASS (6.3.4)

BRASS analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints.

breakdancer (1.4.5)

provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

breseq (0.35.1)

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (<20 Mb).

bsmap (2.90)

BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.

busco (4.1.3)

BUSCO completeness assessments employ sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB ( to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content.

bwa (0.7.17)

BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome.

bwa-mem2 (2-2.1)

The next version of the bwa-mem algorithm in bwa.

Canu (2.1)

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). Canu will correct the reads, then trim suspicious regions (such as remaining SMRTbell adapter), then assemble the corrected and cleaned reads into unitigs.

Canvas (1.40)

Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data.

casper (0.8.2)

CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

caveman (1.13.9)

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples

ceas (1.0.2)

Cis-regulatory Element Annotation System is a tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors.

cellprofiler (3.1.8)

An open-source application for biological image analysis

cellranger (5.0.1)

Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression.

Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.

Cell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells.

cellsnp (0.3.2)

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

cellsnp-lite (1.2.0)

Efficient genotyping bi-allelic SNPs on single cells

cellxgene (0.15.0)

cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas.

cgpBattenberg (3.5.3)

Detect subclonality and copy number in matched NGS data

ChIPseeqer (2.1)

ChIPseeqer is an integrative, comprehensive, fast and user-friendly computational framework for in-depth analysis of ChIP-seq datasets. It combinse several computational tools in order to create easily customized workflows that can be adapted to the user’s needs and objectives.

ChromHMM (1.22)

ChromHMM is software for learning and characterizing chromatin states.

cicero (1.4.0)

an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

circexplorer2 (2.3.8)

A combined strategy to identify circular RNAs (circRNAs and ciRNAs)

circlator (1.5.5)

A tool to circularize genome assemblies

circos (0.69-9)

Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. Also, Circos is useful to visualize any type of information that benefits from a circular layout. Thus, although it has been designed for the field of genomics, it is sufficiently flexible to be used in other data domains.

circtools (

Circtools is a modular, Python3-based framework for circRNA-related tools that unifies several functionalities in single command line driven software. The command line follows the circtools subcommand standard that is employed in samtools or bedtools. Currently, circtools includes modules for detecting and reconstructing circRNAs, a quick check of circRNA mapping results, RBP enrichment screenings, circRNA primer design, statistical testing, and an exon usage module.

clark (1.2.5)

A method based on a supervised sequence classification using discriminative k-mers

clinEff (1.0h)

ClinEff is a professional version of the SnpEff and SnpSift packages, suitable for production in clincal labs. ClinEff combines the flexibility of multiple SnpEff/SnpSift commands with simplicity of running one program to perform all the annotations at once (i.e. in a single pass). It is highly customizable and can be taylored to specific pipeline needs in Clinical production environments.

cnvkit (0.9.8)

Copy number variant detection from targeted DNA sequencing

cnvnator (0.4.1)

CNVnator is a tool for CNV discovery and genotyping from depth of read mapping.

conpair (0.2)

Concordance and contamination estimator for tumor–normal pairs

CREST (1.0.1)

CREST (Clipping Reveals Structure) is an algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data.

crispresso (2.0.44)

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

crossmap (0.4.0)

CrossMap is a program for convenient conversion of genome coordinates between different assemblies (e.g. mm9->mm10). It can convert SAM, BAM, bed, GTF, GFF, wig/bigWig, and VCF files

csvkit (1.0.5)

csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.

ctk (1.1.3)

The CLIP Tool Kit (CTK) is a software package that provides a set of tools for analysis of CLIP data starting from the raw reads generated by the sequencer.

cufflinks (2.2.1)

Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

cutadapt (3.0)

cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.

danpos (2.2.2)

A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2

DeepM6A (0.1)

DeepM6A application implements a deep-learning-based algorithm for predicting potential DNA 6mA sites de novo from sequence at single-nucleotide resolution. Application of this tool to three representative model organisms, Arabidopsis thaliana, Drosophila melanogaster and Escherichia coli, demonstrated that it supercedes the conventional k-mer-based approaches in both accuracy and performance.

deepsignal (0.1.8)

A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads.

deeptools (3.5.0)

deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments.

deepvariant (1.1.0)

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

defuse (0.8.1)

deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.

delly (0.8.7)

DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.


DETONATE is a tool for evaluation of de novo transcriptome assemblies from RNA-Seq data. It consists of two component packages, RSEM-EVAL and REF-EVAL. RSEM-EVAL is a reference-free evaluation method based on a novel probabilistic model that depends only on an assembly and the RNA-Seq reads used for its construction. REF-EVAL is a toolkit of reference-based measures.

DNAnexus (0.300.1)

DNAnexus is a cloud-based commercial solution for next-generation sequence analysis and visualization. It has a command-line interface (CLI) which can be used to log in to the DNAnexus platform, upload and navigate data, and launch analyses.

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.

dropest (0.8.6)

Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements.

dropseq (2.4.0)

Drop-seq is a technology that allows biologists to analyze genome-wide gene expression in thousands of individual cells in a single experiment.

drseq (2.2.0)

Dr.seq is a QC pipeline for Drop-seq data

ea-utils (r822)

Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc.

EGA (3.3.0)

A download client for the European Genome-phenome Archive (EGA). The EGA is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies.

This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data.

EPACTS (3.2.6)

EPACTS (Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers.

epic2 (0.0.41)

Chip-Seq broad peak/domain finder based on SICER

EricScript (0.5.5)

EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data.

exomiser (12.1.0)

The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file.

express (1.5.1)

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

fastqc (0.11.9)

It provide quality control functions to next gen sequencing data.

fastqtools (0.8.3)

fastq-tools a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

fastq_screen (0.14.0)

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

fastxtoolkit (0.0.14)

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

fcgene (1.0.7)

FCgene is a Format Converting tool for genotyped Data (e.g.PLINK-MACH,MACH-PLINK)

flappie (2.1.3)

Basecall Fast5 reads using flip-flop basecalling.

flashpca (2.0)

FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data, similar to smartpca from EIGENSOFT ( and shellfish ( FlashPCA is based on the library.

Flexbar (2.5.0)

Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta and fastq format, e.g. from Illumina and the Roche 454 platform

flye (2.8-1)

Fast and accurate de novo assembler for single molecule sequencing reads

fqtools (2.0)

Tools for manipulating fastq files

freebayes (1.3.5)

Bayesian haplotype-based polymorphism discovery and genotyping

freec (11.6)

Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data

FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased samples.


GATK, from the Broad Institute, is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

gem (3.4)

High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data

Gemini (0.30.2)

GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very powerful system for exploring genetic variation for for disease and population genetics.

GEMMA (0.98.1)

GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS).

The Genome Browser Mirror Fragments is a mirror of the UCSC Genome Browser. The URL is Users can also access the MySQL databases, supporting files directly, and a huge number of associated executables.

genomestrip (2.00.1982)

Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.

genoml (1.0.3)

GenoML is an Automated Machine Learning tool that optimizes machine learning pipelines for genomic data. GenoML will automate the most tedious part of machine learning by intelligently exploring thousands of possible models to find the best one for your data.

genrich (0.6)

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

Gistic (2.0.23)

Facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.

gmap-gsnap (2019-09-12)

A Genomic Mapping and Alignment Programs

gridss (2.9.4)

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

gtool (0.7.5)

GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. GTOOL can be used to (a) generate subsets of genotype data, (b) to convert genotype data between the PED file format and the FILE FORMAT used by SNPTEST and IMPUTE.

guppy (4.2.2)

Local accelerated basecalling for Nanopore data

gvcfgenotyper (2019.02.26)

A utility for merging and genotyping Illumina-style GVCFs.

Hail (0.2.61)

Hail is an open-source, scalable framework for exploring and analyzing genomic data. (0.3.7)

A set of programs based on htslib to benchmark variant calls against gold standard truth datasets.

hgvs (1.5.1)

The hgvs package provides a Python library to facilitate the use of genome, transcript, and protein variants that are represented using the Human Genome Variation Society (varnomen) recommendations. To use, type module load hgvs prior to calling python.

hicexplorer (3.5.1)

Tools to process, normalize and visualize Hi-C data

hichipper (0.7.7)

hichipper is a preprocessing and QC pipeline for HiChIP data. This package takes output from a HiC-Pro run and a sample manifest file (.yaml) that coordinates optional high-quality peaks (identified through ChIP-Seq) and restriction fragment locations (see folder here) as input and produces output that can be used to 1) determine library quality, 2) identify and characterize DNA loops and 3) interactively visualize loops.

hicpro (2.11.4)

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hint (2.27)

a computational method to detect CNVs and Translocations from Hi-C data.

hisat (

HISAT is a fast and sensitive spliced alignment program which uses Hierarchical Indexing for Spliced Alignment of Transcripts.

HLA-LA (1.0.1)

Fast HLA type inference from whole-genome data. Previously known as HLA-PRG-LA.

HMMRATAC (1.2.10)

HMMRATAC peak caller for ATAC-seq data

homer (4.11.1)

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis.

hrdetect (20190829)

Hrdetect is a tool for detection and analysis of homologous recombination deficiency signatures. It was developed to accurately detect BRCA1/BRCA2-deficient samples.

htgts (2)

High-Throughput Genome-Wide Translocation Sequencing pipeline

htseq (0.11.4)

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

humann (3.0.0-alpha.3)

HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).

icgc-get (0.6.1)

icgc-get provides a unified interface to the many sources of data from the International Cancer Genome Consortium.

IDBA (1.1.3)

IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k to perform the assembling task. For all of them, it is very crucial to find a specific value of k. If k is too large, there will be a lot of gap problems in the graph. If k is too small, there will a lot of branch problems. IDBA uses not only one specific k but a range of k values to build the iterative de Bruijn graph. It can keep all the information in graphs with different k values.

idep (0.81)

iDEP (integrated Differential Expression and Pathway analysis) is shiny application for analyzing RNA-seq data

IDR (2.0.3)

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. The IDR method compares a pair of ranked lists of identifications (such as ChIP-seq peaks).

IGV (2.8.9)

The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

IGVTools (2.8.9)

IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted.

IMPUTE (2.3.2)

Impute is a program for estimating ("imputing") unobserved genotypes in SNP association studies.

InterVar (2.1.2, 2.1.3)

In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published updated standards and guidelines for the clinical interpretation of sequence variants with respect to human diseases on the basis of 28 criteria. However, variability between individual interpreters can be extensive because of reasons such as the different understandings of these guidelines and the lack of standard algorithms for implementing them, yet computational tools for semi-automated variant interpretation are not available. To address these problems, InterVar implements these criteria to help human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria.


iSAAC is an ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller)

iva (1.0.8)

IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

Jacquard (0.4.2)

Jacquard makes it easier to analyze multi-patient tumor-normal datasets especially when using multiple vairant callers. It transforms the dialects of different variant callers into a controlled vocabulary of tags with a consistent representation of values. Furthermore, it intelligently merges VCFs from different patients and callers to create a single, unified VCF across your dataset.


JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets.

Juicer (1.6)

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

jvarkit (20200713)

Java tools for bioinformatics

kaiju (1.7.3)

Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA.

Katuali (20190821)

Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data.

KMC (3.1.0)

KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files

KmerGenie (1.7048)

KmerGenie estimates the best k-mer length for genome de novo assembly.

kneaddata (0.7.0)

KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

kraken (2.1.1)

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies

KrakenUniq (0.5.8)

KrakenUniq is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It combines the fast k-mer-based classification of Kraken (Wood and Salzberg, Genome Biology 2014) with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory.

laser (2.04)

LASER is a program to estimate individual ancestry by directly analyzing shotgun sequence reads without calling genotypes.

leafcutter (0.2.7)

Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples.

lefse (1.0.8)

LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.

locuszoom (1.3)

LocusZoom is designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates

lofreq (2.1.5)

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.

lumpy (0.2.13)

A probabilistic framework for structural variant discovery.

mach2qtl (1.1.3)

mach2qtl uses dosages/posterior probabilities inferred with MACH as predictors in a linear regression to test association with a quantitative trait

macs (

Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction.

mafft (7.475)

Multiple alignment program for amino acid or nucleotide sequences


MAGeCK is Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. It demonstrates better performance compared with other methods, identifies both positively and negatively selected genes simultaneously, and reports robust results across different experimental conditions.

mageck-vispr (0.5.4)

MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.

MAGGIE (0.3.4)

MAGGIE provides a framework for identifying DNA sequence motifs mediating transcription factor binding and function.

magicblast (1.5.0)

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

MAJIQ (2.1-patched)

Modeling Alternative Junction Inclusion Quantification. MAJIQ and Voila are two software packages that together define, quantify, and visualize local splicing variations (LSV) from RNA-Seq data.

manorm (1.1.4)

MAnorm is for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.

manta (1.6.0)

Structural variant and indel caller for mapped sequencing data

maps (1.1.0)

a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.

mapsplice (2.2.1)

Accurate mapping of RNA-seq reads for splice junction discovery

mash (2.2)

mash is a command line tool and library to provide fast genome and metagenome distance estimation using MinHash. Only command line tool is installed

medaka (1.2.0)

medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly.

medusa (1.6)

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

MEGAHIT (1.2.9)

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG construction.

megalodon (2.2.9)

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transcriptome.

MEGAN (6_20_8)

MEtaGenome ANalyzer that takes a file of reads and a Blast output from comparison against a reference genome, and automatically calculate a taxonomic classification of the reads and if desired, a functional classification.

Meryl (0.0)

Meryl: a genomic k-mer counter (and sequence utility) with nice features. It is built into the Celera Assembler and is also available as a stand-alone application. Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.

metabat (2.13)

MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data

metal (2018-08-28)

The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.

metaphlan (3.0.6)

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

minialign (0.6.0)

fast and accurate alignment tool for PacBio and Nanopore long reads

miniasm (0.3.r179)

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

minimac (4 (1.0.1))

minimac is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. 'mini' refers to the low amount of computational resources it needs.

minimap2 (2.17)

Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR).

mirdeep2 (

miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.

misopy (0.5.4)

MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data

mitosuite (1.0.9b)

mitosuite is a graphical tool for human mitochondrial genome profiling in massively parallel sequencing

mixcr (3.0.13)

MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.

mocat2 (current)

a package for analyzing metagenomics datasets

MonoVar (20200403)

Monovar is a statistical method for detecting and genotyping single-nucleotide variants in single-cell data. It takes onto account an allelic dropout, false-positive errors and a nonuniformity of coverage.

morgan (3.4)

MORGAN (Monte Carlo Genetic Analysis)

mosdepth (0.3.0)

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

msCentipede is an algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (Dnase-seq, ATAC-seq)

mtoolbox (1.1)

A bioinformatics pipeline aimed at the analysis of mitochondrial DNA (mtDNA) in high throughput sequencing studies.

multiqc (1.9)

aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report

MuSE (1.0~rc-c)

MuSE is an approach to somatic variant calling based on the F81 Markov substitution model for molecular evolution, which models the evolution of the reference allele to the allelic composition of the matched tumor and normal tissue at each genomic locus.

muTect (1.1.7)

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

MutSig (1.41)

MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.

nanopolish (0.13.2)

nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

neusomatic (0.2.1)

NeuSomatic is based on deep convolutional neural networks for accurate somatic mutation detection. With properly trained models, it can robustly perform across sequencing platforms, strategies, and conditions. NeuSomatic summarizes and augments sequence alignments in a novel way and incorporates multi-dimensional features to capture variant signals effectively. It is not only a universal but also accurate somatic mutation detection method.

NGMLR (0.2.7)

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations.

ngscheckmate (1.0.0)

NGSCheckMate validates nucleotide sequencing sample identity from fastq, BAM, or VCF files.

ngsplot (2.63)

ngsplot is an easy-to-use global visualization tool for next-generation sequencing data.

novocraft (4.03.02)

Package includes aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.

opera-lg (2.0.6)

OPERA (Optimal Paired-End Read Assembler) is a sequence assembly program. It uses information from paired-end/mate-pair/long reads to order and orient the intermediate contigs/scaffolds assembled in a genome assembly project, in a process known as Scaffolding.

parpipe (79b1aab)

Complete analysis pipeline for PAR-CLIP data

PartekFlow (

Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.

pbsuite (15.8.24)

The PBSuite contains two projects created for analysis of Pacific Biosciences long-read sequencing data: PBHoney and PBJelly. PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants. PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.

peakranger (1.18)

A ChIP-Seq peak caller for narrow and broad peaks

pear (0.9.11)

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

peddy (0.4.6)

peddy is used to compare sex and familial relationships given in a PED file with those inferred from a VCF file

PEPATAC (0.8.3)

PEPATAC is a robust pipeline for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) built on a loosely coupled modular framework. It may be easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches.

PePr (1.1.24)

PePr is a ChIP-Seq Peak-calling and Prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution.

picard (2.25.0)

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

picrust (2.3.0-b)

PICRUSt is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.

pindel (0.2.5)

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pirs (2.0.2)

Profile-based Illumina paired-end Read Simulator

plastid (0.4.8)

Position-wise analysis of sequencing and genomics data

Platypus (0.8.1)

tool for variant-detection in high-throughput sequencing data.

plink (2.3-alpha)

PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

plinkseq (0.10)

library for the analysis of genetic variation data

pomoxis (0.2.3)

Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. Notably tools are included for generating and analysing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies.

porechop (0.2.4)

Trim/demultiplex Oxford Nanopore reads

poretools (0.6.1a1)

Poretools is a toolkit for manipulating and exploring nanopore sequencing data sets. Poretools operates on individual FAST5 files, directory of FAST5 files, and tar archives of FAST5 files.

preseq (3.1.1)

predicting library complexity and genome coverage in high-throughput sequencing

PRINSEQ (0.20.4)

PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data.

proseq (2.0)

proseq-2.0 is a pipeline for preprocesses and alignment of run-on sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing

PROVEAN (1.1.5)

PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

purge_haplotigs is a pipeline to help with curating heterozygous diploid genome assemblies.

pvactools (1.5.5)

pVACtools is a cancer immunotherapy suite consisting of pVACseq, pVACfuse, pVACvector

pychopper (2.4.0)

Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.

pyclone (0.13.1)

PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples.

pyDNase (0.3.0)

pyDNase is a suite of tools for analysing DNase-seq data - pyDNase comes with several analysis scripts covering several common use cases of DNase-seq analysis, and also an implementation of the Wellington, Wellington 1D, and Wellington-boostrap footprinting algorithms.

PyLOH (1.4.3)

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

qcat (1.1.0)

qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.

qctool (2.1c03c1f)

QCTOOL is a command-line utility program for basic quality control of gwas datasets.

QoRTs (1.3.6)

The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets.

qualimap (2.2)

A platform-independednt application written in Java and R that provides both a GUI and a co mmand-line interface to facilitate the quality control of alignment sequencing data.

quast (5.0.2)

QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. The package includes the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, and Icarus, interactive visualizer for these tools.

racon (1.4.3)

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

raremetal (4.15.1)

RAREMETAL is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data.

Rcorrector (

Rcorrector implements a k-mer based method to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read.

READemption (1.0.1)

RNA-Seq pipeline including alignment, coverage tracks, quantitation, and differential expression analysis.

RepeatMasker (4.1.1)

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program.

repeatmodeler (2.0.1)

RepeatModeler is a de novo transposable element (TE) family identification and modeling package. RepeatModeler assists in automating the runs of the various algorithms given a genomic database, clustering redundant results, refining and classifying the families and producing a high quality library of TE families suitable for use with RepeatMasker and ultimately for submission to the Dfam database (

rgt (0.12.3)

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

ricopili (2019_Jun_25.001 )

RICOPILI stands for Rapid Imputation and COmputational PIpeLIne for GWAS.

rilseq (0.75)

RILseq computational protocol

rnapeg (current)

RNApeg is required to generate a junctions file for use by CICERO

rnaseqc (2.3.6)

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data.

rockhopper (2.0.3)

Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files)

RSD (1.1.7)

Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes.

rsem (1.3.3)

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

rseqc (4.0.0)

Rseqc comprehensively evaluate RNA-seq datasets generated from clinical tissues or other well annotated organisms such as mouse, fly and yeast.

rvtests (2.1.0)

Rare Variant tests is a flexible software package for genetic association studies. It is designed to support unrelated individual or related (family-based) individuals

sailfish (0.10.0)

Sailfish is a tool for transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All that is needed to run sailfish is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your RNA-Seq reads.

salmon (1.4.0)

a tool for quantifying the expression of transcripts using RNA-seq data.

SalmonTE (0.4)

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances.

sambamba (0.8.0)

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.

samblaster (0.1.24)

samblaster is a program for marking duplicates and finding discordant/split read pairs in read-id grouped paired-end SAM files. When marking duplicates, samblaster will use about 20MB per 1M read pairs. In a read-id grouped SAM file all alignments for a read-id (QNAME) are continuous. Aligners naturally produce such files. They can also be created by sorting a SAM file by read-id.

samtools (1.11)

The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library.

scallop (0.10.4)

Scallop is a reference-based transcript assembler.

scalpel (0.5.4)

Bioinformatics pipeline for discovery of genetic variants from NGS reads.

ScanIndel (1.3)

ScanIndel is a python program to detect indels (insertions and deletions) from NGS data by re-align and de novo assemble soft clipped reads.

scanpy (1.4.4)

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

schism (1.1.3)

Subclonal Hierarchy Inference from Somatic Mutations

Scramble (1.0.1)

Scramble is a mobile element insertion (MEI) detection tool. It identifies clusters of soft clipped reads in a BAM file, builds consensus sequences, aligns to representative L1Ta, AluYa5, and SVA-E sequences, and outputs MEI calls.

segemehl (0.3.4)

Segemehl is a short read aligner that allows local alignment and can align reads obtained after bisulfite treatment.

seqan (2.4.0)

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. This package also contains a suite of apps, including Fiona, Gustaf, Mason, RazerS 3, Yara, SeqAn T-Coffee, Stellar, and searchjoin.

seqkit (0.15.0)

A cross-platform toolkit for FASTA/Q file manipulation

seqlinkage (1.0)

SEQLinkage implements a collapsed haplotype pattern (CHP) method to generate markers from sequence data for linkage analysis.

seqoutbias (1.1.3)

Correct aligned HTS read counts for enzyme bias and mappability.

seqtk (1.3)

seqtk is a toolkit for processing sequences in FASTA/Q formats

Sequenza-utils is The supporting python library for the sequenza R package. Sequenza is a project the estimate purity/ploidy and copy number alteration from tumor sequencing experiments. Sequenza-utils provide command lines programs to transform common NGS file type, such as BAM, pileup and VCF, to input files for the R package

sga (0.10.15)

SGA (String Graph Assembler) is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. It is based on Gene Myers' string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads.

SGA-ICE (20170728)

The script SGA-ICE (SGA-Iteratively Correcting Errors) implements iterative error correction by using modules from the String Graph Assembler (SGA).

shapeit (4.1.3)

SHAPEIT is a fast and accurate haplotype inference software

shmlast (1.2.1)

shmlast is a reimplementation of the Conditional Reciprocal Best Hits algorithm for finding potential orthologs between a transcriptome and a species-specific protein database. It uses the LAST aligner and the pydata stack to achieve much better performance while staying in the Python ecosystem.

shrimp (2_2_3)

SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.

sicer (2-1.0.2)

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

sickle (1.33)

A windowed adaptive trimming tool for FASTQ files using quality

SIFT (6.2.1)

SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids.

slamdunk (0.4.3)

SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

smalt (0.7.6)

SMALT efficiently aligns DNA sequencing reads with a reference genome.

smart (2.2.8)

Specific Methylation Analysis and Report Tool (SMART) uses the signal from bisulfite sequencing experiments across multiple samples to identify genome segments with similar methylation secificities.

smc++ (1.13.1)

SMC++ is a program for estimating the size history of populations from whole genome sequence data.

SMRT® Analysis is a bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio® and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.

snaptools (1.4.8)

A module for working with snap files in Python.

sniffles (1.0.11)

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.

snippy (4.4.1)

snippy is a tool for rapid haploid variant calling and core genome alignment

snp2hla (1.0.3)

SNP2HLA is a tool to impute amino acid polymorphisms and single nucleotide polymorphisms in human luekocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6.

snpEff (5.0)

snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

snptest (2.5.4beta3)

SNPTEST is a program for the analysis of single SNP association in genome-wide studies. The tests implemented include * Binary (case-control) phenotypes, single and multiple quantitative phenotypes * Bayesian and Frequentist tests * Ability to condition upon an arbitrary set of covariates * Various different methods for the dealing with imputed SNPs. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL.

SomaticSeq (3.1.0)

SomaticSeq is an ensemble approach to accurately detect somatic mutations. It incorporates multiple somatic mutation caller(s) to obtain a combined call set, and then uses machine learning to distinguish true mutations from false positives from that call set.

somaticsniper (

The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format.

sortmeRNA (3.0.3)

SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files specified by the user.

spaceranger (1.2.2)

10x pipeline for processing Visium spatial RNA-seq data

spacy (2.2.3)

advanced Natural Language Processing (NLP) in Python

spades (3.14.1)

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.

speedseq (0.1.2-20180208-4e60002)

SpeedSeq is a genome analysis platform designed for rapid whole-genome variant detection and interpretation

spruce (20180606)

SPRUCE (Somatic Phylogeny Reconstruction using Combinatorial Enumeration) is an algorithm for inferring the clonal evolution of single-nucleotide and copy-number variants given multi-sample bulk tumor sequencing data.

sratoolkit (2.10.9)

The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.

SRST2 (0.2.0)

SRST2 is a a read mapping-based tool for rapid molecular typing of bacterial pathogens. It allows fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment.

stampy (1.0.32)

Short read aligner

STAR (2.7.6a)

Spliced Transcripts Alignment to a Reference

STAR-Fusion (1.9.1)

Transcript fusion detection

STREAM (20180816)

STREAM stands for Single-cell Trajectories Reconstruction, Exploration And Mapping ofomics data. It is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.

strelka (2.9.10)

Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

stringtie (2.1.4)

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genome assembly to help with transcript assembly.

ST_pipeline (1.7.6)

The Spatial Transcriptomics (ST) pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics technology in FASTQ format to generate datasets for down-stream analysis. The ST pipeline can also be used to process single cell RNASeq data as long as a file with barcodes identifying each cell is provi ded. The ST Pipeline has been optimized for speed, robustness and it is very easy to use with many parameters to adjust all the settings. The ST Pipeline is fully parallel and has constant memory use.

subread (2.0.1)

High-performance read alignment, quantification and mutation discovery

supernova (2.1.1)

Supernova generates highly-contiguous, phased, whole-genome de novo assemblies from a Chromium-prepared library.

suppa (2.3)

Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

SURVIVOR (1.0.5)

SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

svclone (0.2.2-13-ge402c3f)

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.

sve (0.1.0)

SVE is a python script based execution engine for Structural Variation (SV) detection and can be used for any levels of data inputs, raw FASTQs, aligned BAMs, or variant call format (VCFs), and generates a unified VCF as its output.

svtk (0.1)

Utilities for consolidating, filtering, resolving, and annotating structural variants.

svtyper (0.1.4)

Svtyper is a Bayesian genotyper for structural variants.

tagit (1.0.8)

Tag(ging) It(erative) of SNVs in multiple populations.

taiji (v1.2.0)

The Taiji software is a versatile genomics data analysis pipeline. It can be used to analyze ATAC-seq, RNA-seq, single cell ATAC-seq and Drop-seq data.

tailseeker (3.1.7-6-g34b5ba9)

Tailseeker is the official pipeline for TAIL-seq, which measures poly(A) tail lengths and 3′-end modifications with Illumina SBS sequencers.

tandemtools (current)

Tool for assessing/improving assembly quality in extra-long tandem repeats

tappas (1.0.3)

A comprehensive computational framework for the analysis of the functional impact of differential splicing

taxonkit (0.5.0)

A Cross-platform and Efficient NCBI Taxonomy Toolkit

telescope (1.0.2)

Single locus resolution of Transposable ELEment expression. Telescope estimates transposable element expression (retrotranscriptome) resolved to specific genomic locations. It directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model.

telseq (0.0.2)

TelSeq is a software that estimates telomere length from whole genome sequencing data (BAMs).

tetoolkit (2.1.4)

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

THetA (0.7-7-g8f93e6c)

Tumor Heterogeneity Analysis (THetA) is an algorithm used to estimate tumor purity and clonal/subclonal copy number aberrations simultaneously from high-throughput DNA sequencing data.

TMAP (3.4.1)

TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by Ion Torrent sequencing technologies.

tophat (2.1.1)

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

TPMCalculator (0.0.4)

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

TransDecoder (5.5.0)

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

transrate (1.0.3)

Transrate is software for de-novo transcriptome assembly quality analysis.

transvar (2.4.0)

TransVar is a versatile annotator for 3-way conversion and annotation among genomic characterization(s) of mutations and transcript-dependent annotation(s).

trimgalore (0.6.6)

Consistent quality and adapter trimming for RRBS or standard FastQ files.

trimmomatic (0.38)

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

trinity (2.11.0)

Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Trinotate (3.2.0)

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

tRNAscan-SE (2.0.0)

tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database

truffle (1.38)

"Fast and accurate shared segment detection and relatedness estimation in un- phased genetic data using TRUFFLE"

TVC (5.10.1)

TVC is the standalone Torrent Variant Caller, part of the Ion Torrent Suite.

umitools (1.1.1)

tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes

varsim (0.8.5)

A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications

vasttools (2.5.0)

A toolset for profiling alternative splicing events in RNA-Seq data.

vcf2maf (1.6.19)

A smarter, more reproducible, and more configurable tool for converting a VCF to a MAF.

vcfanno (0.3.2)

annotate a VCF with other VCFs/BEDs/tabixed files

vcflib (1.0.1)

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

vcftools (0.1.16)

VCFtools contains a Perl API ( and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc.

velvet (1.2.10)

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454

VEP (103.1)

VEP (Variant Effect Predictor) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

verifybamid (1.1.3)

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps.

vg (1.25.0)

Tools for working with genome variation graphs

viper (0-20181127-b74e0bc-p1)

VIPER combines the use of several dozen RNA-seq tools, suites, and packages to create a complete pipeline that takes RNA-seq analysis from raw sequencing data all the way through alignment, quality control, unsupervised analyses, differential expression, and downstream pathway analysis

viral-ngs (1.22.1)

viral-ngs comprises a set of viral genomics analysis pipelines developed by the Broad Institute

vireosnp (0.5.1)

Demultiplexing pooled scRNA-seq data without genotype reference

VIRTUS (1.2.1)

Bioinformatics pipeline for viral transcriptome detection.

vsearch (2.14.2)

VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.

vt (0.57721)

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

xHLA (2018-04-04)

The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. xHLA iteratively refines the mapping results at the amino acid level to achieve high typing accuracy for both class I and II HLA genes.

XHMM (2016-01-04)

XHMM uses principal component analysis (PCA) normalization and a hidden Markov model (HMM) to detect and genotype copy number variation (CNV) from normalized read-depth data from targeted sequencing experiments.

xwas (3.0)

XWAS (chromosome X-Wide Analysis toolSet) is a software suite for the analysis of the X chromosome in association analyses and similar studies.

back to top

3DSlicer (4.10.2)

A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy.

AFNI (current)

AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

ANTs (2.3.2)

Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data.

B-SOiD (1.3)

B-SOiD (Behavioral Segmentation in Deeplabcut) is an unsupervised learning algorithm that serves to discover and classify behaviors that are not pre-defined by users. It segregates statistically different, sub-second rodent behaviors with a single bottom-up perspective video cameraR by performing a novel expectation maximization fitting of Gaussian mixture models on t-Distributed Stochastic Neighbor Embedding (t-SNE).

baracus (1.1.4)

Baracus predicts brain age, based on data from Freesurfer. It combines data from cortical thickness, cortical surface area, and subcortical information

broccoli (1.0.1)

Pipeline for fast analysis of fMRI data

Bsoft (1.9.0)

Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages.

c3d (1.1.0)

C3D is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling.

cisTEM (1.0.0-beta)

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

cmtk (3.3.1)

CMTK is a Software toolkit for computational morphometry of biomedical images. CMTK provides a set of command line tools for processing and I/O.

Tools to browse, download, explore, and analyze data from the Human Connectome Project (HCP). Allows users to compare their own data to that of the HCP.

CTF (6.1.14-beta)

The CTF MEG software has two main roles: - Provide a human-machine interface to the CTF MEG elec- tronics to collect MEG and/or EEG data. - Provide a tool for reviewing and (to a limited extent) ana- lyzing the MEG and/or EEG data acquired by the CTF MEG system.

ctffind (4.1.14)

Programs for finding CTFs of electron micrographs

dcm2niix (1.0.20200331)

DICOM to NIfTI converter

DeepLabCut (;; 2.2b7)

DeepLabCut is an open source toolbox that builds on a state-of-the-art human pose estimation algorithm. It allows training of a deep neural network by using limited training data to precisely track user-defined features, so that the human labeling accuracy will be matched.

dynamo (1.4.01)

Dynamo is a software environment for subtomogram averaging of cryo-EM data.

elastix (4.9)

a toolbox for rigid and nonrigid registration of images.

EMAN2 (2.31)

EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.

fastsurfer (c5e9677)

Fastsurfer is a neuroimaging pipeline based on deep learning.

Fiji (1.52f)

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.

fitlins (0.8.0)

Fitlins fits linear models to BIDS neuroimaging datasets.

fmriprep (20.2.1)

A Robust Preprocessing Pipeline for fMRI Data

Frealign (9.11_151031)

Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.

Freesurfer (7.1.1)

Freesurfer is a set of automated tools for reconstruction of the brain's cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

FSL (6.0.4)

FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data.

Gctf (1.06)

Gctf provides accurate estimation of the contrast transfer function (CTF) for near-atomic resolution cryo electron microscopy (cryoEM) reconstruction using GPUs.

Huygens (20.10)

Huygens is an image restoration, deconvolution, resolution and noise reduction. It can process images from all current optical microscopes, including wide-field, confocal, Nipkow (scanning disk confocal), multiple-photon, and 4Pi microscopes.

IMOD (4.10.10)

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

mango (4.1)

Mango (Multi-image Analysis GUI) is a viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.

MIPAV (10.0.0)

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy.

MotionCor2 (1.4.0)

MotionCor2 is a multi-GPU accelerated program that provides iterative, patch-based motion detection combining spatial and temporal constraints and dose weighting for both single particle and tomographic cryo-electon microscopy images.

mriqc (0.16.0)

MRIQC is an MRI quality control tool

mrtrix (3.0.2)

MRtrix provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI.

qsiprep (0.8.0)

qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data.

RELION (3.1.1)

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

ResMap (1.9)

ResMap (Resolution Map) is a Python (NumPy/SciPy) application with a Tkinter GUI and a command-line interface. It is a software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM).

SAMsrcV3 (20180713-c5e1042)

Synthetic Aperture Magnetometry - The SANsrcV3 suite implements the latest advances in MEG source localization.

SimNIBS (3.1.1)

SimNIBS is a free software package for the Simulation of Non-invasive Brain Stimulation. It allows for realistic calculations of the electric field induced by transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS).

spacy (2.2.3)

advanced Natural Language Processing (NLP) in Python

SPHIRE (1.1)

SPHIRE (SPARX for High-Resolution Electron Microscopy) is an open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. It allows fast and reproducible structure determination from cryo-EM images.

Spinal Cord Toolbox (SCT), a comprehensive software dedicated to the processing of spinal cord MRI data. SCT builds on previously-validated methods and includes state-ofthe-art MRI templates and atlases of the spinal cord, algorithms to segment and register new data to the templates, and motion correction methods for diffusion and functional time series.

spm12 (7870)

The (S)tatistical (P)ara(M)etric application analyzes brain imaging data.

summovie (1.0.2)

Summovie calculates movie frame sums, using the alignment results from a prior run of Unblur.

TeraStitcher (1.11.10)

TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power.

tesseract (4.1.1)

tesseract is a open source commercial quality OCR engine developed at Google.

topaz (0.2.5)

topaz is a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models.

TORTOISE (3.2.0)

(Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble) The TORTOISE software package is for processing diffusion MRI data.

tvb (1.5.8)

The Virtual Brain (TVB) scientific library has the purpose of offering modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains

unblur (1.0.2)

Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion.

xcpengine (1.2.3)

xpcEngine performs denoising and estimation of Functional Connectivity on fMRI datasets

back to top

AdmixTools (6.0)

ADMIXTOOLS is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

admixture (1.3.0)

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

AncestryMap (6210)

AncestryMap is a software package that allows finding skews in ancestry that are potentially associated with disease genes in recently mixed populations.

bali-phy (3.5)

BAli-Phy is MCMC software developed by Ben Redelings with Marc Suchard for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming.

Beagle (5.1_18May20)

Beagle is a package for imputing genotypes, inferring haplotype phase, and performing genetic association analysis. BEAGLE is designed to analyze large-scale data sets with hundreds of thousands of markers genotyped on thousands of samples.

beagle-lib (3.1.2)

BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.
module name: beagle-lib

BEAST (1.10.4,2.6.2)

BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences.

CD-HIT (4.6.8)

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

eigensoft (7.2.1)

The EIGENSOFT package combines functionality from population genetics methods and EIGENSTRAT stratification correction method.

FastQTL (2.184)

In order to discover quantitative trait loci (QTLs), multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. FastQTL implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing.

FastTree (2.1.10)

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

GCTA (1.92.3beta3)

GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits.

gubbins (2.3.4)

Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

hyphy (2.5.27)

HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.

iqtree (2.1.2)

Efficient phylogenomic software by maximum likelihood

king (2.2.5)

KING is a toolset to explore genotype data from a genome-wide association study (GWAS) or a sequencing project. KING can be used to check family relationship and flag pedigree errors by estimating kinship coefficients and inferring IBD segments for all pairwise relationships.

LDpred (1.0.11)

LDpred is a Python based software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium (LD).

loki (2.4.7_4)

Loki is a linkage analysis package, primarily for large and complex pedigrees, which uses Markov chain Monte Carlo (MCMC) techniques to avoid many of the computational problems that prevent exact computational methods being used for large pedigrees.

MALDER (1.0)

MALDER is a Modified version of ALDER that has been modified to allow multiple admixture events. ALDER computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture described in: Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, and Berger B. Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium. Genetics, 2013.

mantra (1)

Transethnic meta-analysis of genomewide association studies

mega2 (6.0.0)

Mega2 is a data-handling program for facilitating genetic linkage and association analyses.

merlin (1.1.2)

MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around.

mothur (1.44.1)

mothur is a tool for analyzing 16S rRNA gene sequences generated on multiple platforms as part of microbial ecology projects.

MrBayes (3.2.7)

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

phase (2.1.1)

infers haplotypes from population genotype data

Phylip (3.696)

Phylip is a package of programs for inferring phylogenies (evolutionary trees). Includes methods for parsimony, distance matrix and likelihood methods.

pplacer (1.1)

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

PRSice (2.3.3)

PRSice is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses.

QIIME (2-2020.11)

QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).

RAxML (8.2.12)

RAxML (randomized axelerated maximum likelihood) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML).

raxml-ng (1.0.0)

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Successor to raxml.

RefinedIBD (17Jan20)

Refined IBD is a software package that detects identity-by-descent segments in phased genotype data. It achieves both computational efficiency and highly accurate IBD segment reporting by searching for IBD in two steps. The first step (identification) uses the GERMLINE algorithm to find shared haplotypes exceeding a length threshold. The second step (refinement) evaluates candidate segments with a probabilistic approach to assess the evidence for IBD.

seqmix (0.1)

SEQMIX is a program that takes advantage of off-targeted sequence reads from exome/targeted sequencing experiments for accurate local ancestry inference.

shapeit (4.1.3)

SHAPEIT is a fast and accurate haplotype inference software

SMR (0.702; 1.03)

SMR integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. It implements methods to test for pleiotropic association between the expression level of a gene and a complex trait of interest using summary-level data from GWAS and expression quantitative trait loci (eQTL) studies (Zhu et al. 2016 Nat Genet).

Solar (8.4.1)

SOLAR-Eclipse is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening.

treemix (1.12)

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.

back to top

fragpipe (14.0)

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger.

Mascot (2.5)

The Mascot search engine uses mass spectrometry data to identify proteins from primary sequence databases. Mascot searches can be run directly on the NIH Mascot server at, or by using the Mascot daemon on your own desktop PC.

maxquant (

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.

metamorpheus (2020.11.23)

MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability.

msfragger (3.1.1)

An ultrafast database search tool for peptide identification in mass spectrometry-based proteomics.

philosopher (3.3.12)

Philosopher is fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery.

back to top

ANTs (2.3.2)

Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data.

CLONET (20171016)

CLONET is a collection of R scripts that allows: computing global DNA admixture (1-purity) and ploidy of tumor DNA samples (each with matched normal sample) from sequencing data (WGS, WES, targeted) computing clonality of each somatic aberration, including somatic copy number aberrations, point mutations, and structural rearrangements nominatig the temporal relation among somatic aberrations and building evolution maps

cmdstan (2.24.1)

Command line interface to stan

Comsol (56)

The COMSOL Multiphysics engineering simulation software environment facilitates all steps in the modeling process − defining your geometry, meshing, specifying your physics, solving, and then visualizing your results.

GAUSS (10)

The GAUSS Mathematical and Statistical System is an easy-to-use data analysis environment based on the fast and powerful GAUSS Matrix Programming Language designed for computationally intensive tasks.

gephi (0.9.2)

gephi is a scientific application for computation of a number of metrics in graph/network analysis.

IDL/ENVI (8.8/5.6)

IDL and ENVI are a complete computing environment for the interactive analysis and visualization of data. IDL integrates an array-oriented language with mathematical analysis and graphical display techniques. ENVI is designed for extracting information from geospatial and medical imagery.

m2clust (1.1.3)

m2clust provides an elegant clustering approach to find clusters in data sets with different density and resolution.

Mathematica (12.2)

Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language.

Matlab (2020b)

MATLAB is an interactive software package for scientific and engineering numeric computation. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an environment where problems and solutions are expressed just as they are written mathematically.

MCL (14-137)

MCL implements Markov cluster algorithm. Among its applications is the assignment of proteins into families based on precomputed sequence similarity information. This approach does not suffer from the problems that normally hinder other protein sequence clustering algorithms, such as the presence of multi-domain proteins, promiscuous domains and fragmented proteins.

Meep (1.17.1)

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with the MPB eigenmode package.

Octave (5.1.0)

GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.

omeClust (1.1.6)

omeClust (previously m2clust) is a clustering method that detects clusters of features using omics data and scores metadata (resolution score) based on their influences in clustering.

PEER (1.3)

PEER stands for probabilistic estimation of expression residuals. It is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.

R (4.0.3)

R (the R Project) is a language and environment for statistical computing and graphics. R is similar to S, and provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).

Rstudio (1.4.1103)

RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

SAS (9.4M6)

Base SAS provides a scalable, integrated software environment specially designed for data access, transformation and reporting.

back to top

blender (2.82)

Blender is the free and open source 3D creation suite. Blender on Biowulf is meant for command-line rendering.

Chimera (1.15.0)

Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

Coot (

Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

Cytoscape (3.8.2)

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Glycosylator (20191122)

Glycosylator is a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its API or GUI. The GUI allows for a quick visual inspection of the glycosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific three-dimensional (3D) glycans on a protein structure using a library of predefined templates.

lammps (29Oct20)

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. It runs on a variety of different computer systems, including single processor systems, distributed-memory machines with MPI, and GPU and Xeon Phi systems. LAMMPS is open source software, released under the GNU General Public License.

Biophysical Neural Network Modeling Software.

OpenBabel (3.0.0)

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

Psi4 (1.2)

Psi4 is an ab-initio electronic structure code that supports various methods for calculating energies and gradients of molecular systems.

Rosetta (2020.46)

The Rosetta++ software suite can perform de novo protein structure predictions, identify low free energy sequences for target protein backbones, predict the structure of a protein-protein complex from the individual structures of the monomer components, incorporate NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction, and more...

Schrodinger (2020.4)

A limited number of Schrödinger applications are available on the Biowulf cluster through the Molecular Modeling Interest Group. Most are available through the Maestro GUI.

VMD (1.9.3)

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. To use, type vmd at the prompt.

back to top

Accurity (20180724)

Accurity is a tool for inference of tumor purity, tumor cell ploidy and absolute allelic copy numbers from tumor-normal WGS data.

alleleCount (4.0.0)

Calculates genotype frequencies of a SNPMatrix. This component tests each SNP for its Hardy-Weinberg equilibrium. If there are NA values, the frequencies of missing value per sample in the input file are calculated.

ANNOgesic (1.0.2)

Processing and integrating RNA-Seq data in order to generate high-resolution annotations is challenging, time consuming and requires numerous different steps. ANNOgesic is a powerful and modular pipeline that provides the required analyses and simplifies RNA-Seq-based bacterial and archaeal genome annotation. It predicts and annotates numerous features, including small non-coding RNAs, with high precision.

anvio (7)

Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics. It brings together many aspects of today’s cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

arriba (1.2.0)

Arriba identifies gene fusions in RNA-Seq data. It also can detect other structural variants in genomic data, such as intron duplications and gene truncations.

augustus (3.3.3)

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

bamcmp (20180719)

bamcmp is a tool for deconvolving host and graft reads. It allows an accurate identification of the contaminating host reads when analyzing DNA-Seq and RNA-Seq data from patient-derived xenograft and circulating tumor cell–derived explant models.

Bamgineer introduces simulated allele-specific copy number variants into exome and targeted sequence data sets

Blast (2.11.0+)

NCBI's well-known sequence database searching program which compares a nucleotide or protein query sequence against all sequences in a database.

blat (3.5)

BLAT is a DNA/Protein Sequence Analysis program that is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more.

blobtools (1.0)

A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.

BOLT-LMM (2.3.4)

The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM)

bwa-mem2 (2-2.1)

The next version of the bwa-mem algorithm in bwa.

cactus (1.2.3)

Cactus is a reference-free whole-genome multiple alignment program.

CAVIAR (2.2)

CAVIAR (CAusal Variants Identication in Associated Regions) is a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants

cellsnp-lite (1.2.0)

Efficient genotyping bi-allelic SNPs on single cells

AQUAS Transcription Factor and Histone ChIP-Seq processing pipeline. The AQUAS pipeline is based off the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specifications (by Anshul Kundaje)

cicero (1.4.0)

an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

circos (0.69-9)

Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. Also, Circos is useful to visualize any type of information that benefits from a circular layout. Thus, although it has been designed for the field of genomics, it is sufficiently flexible to be used in other data domains.

CITE-seq-Count is a python package that counts antibody TAGS. It handles the data from both the Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seqi) and/or Cell Hashing experiment.

Clinker (1.32)

Clinker is a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc), that can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz.

clustalo (1.2.4)

Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for proteins and DNA/RNA. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.

ClustalW (2.1)

ClustalW is a general-purpose multiple alignment program for DNA or protein sequences.

CutRunTools (20191001)

CutRunTools is a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CutRun primary cleavage data. CutRunTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CutRun.

DeconSeq (0.4.3)

The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

DeepM6A (0.1)

DeepM6A application implements a deep-learning-based algorithm for predicting potential DNA 6mA sites de novo from sequence at single-nucleotide resolution. Application of this tool to three representative model organisms, Arabidopsis thaliana, Drosophila melanogaster and Escherichia coli, demonstrated that it supercedes the conventional k-mer-based approaches in both accuracy and performance.

deepsea (0.94c)

DeepSEA is a deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity. DeepSEA can accurately predict the epigenetic state of a sequence, including transcription factors binding, DNase I sensitivities and histone marks in multiple cell types, and further utilize this capability to predict the chromatin effects of sequence variants and prioritize regulatory variants.

diamond (2.0.5)

DIAMOND is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity.

DNAWorks (3.2.4)

DNAWorks is a computer program that automates the design of oligonucleotides for gene synthesis by PCR-based gene assembly. The program requires simple input information: an amino acid sequence of the target protein or a DNA sequence, and a desired annealing temperature. It is a web-based tool available at

Eagle (2.4)

Eagle performs a reference-based haplotype phasing. It attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as the Haplotype Reference onsortium; HRC) using a new data structure based on the positional Burrows-Wheeler transform.

emim (3.22)

Estimation of Maternal, Imprinting and interaction effects using Multinomial modeling

EukRep (20180308)

Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, eukaryotic genomes shoould be recovered from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. EukRep is a kmer- and SVM-based strategy for eukaryotic sequence identification from environmental samples.

exonerate (2.4.0)

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

Expansion Hunter: a tool for estimating repeat sizes. There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat.

ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs). EHdn is intended for analysis of a collection of BAM/CRAM files containing alignments of short (100-200bp) reads.

fastp (0.20.1)

A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

FitHiChIP (6.0)

FitHiChIP is a computational method for identifying chromatin contacts among regulatory regions such as enhancers and promoters from HiChIP/PLAC-seq data. FitHiChIP jointly models the non-uniform coverage and genomic distance scaling of HiChIP data, captures previously validated enhancer interactions for several genes including MYC and TP53, and recovers contacts genome-wide that are supported by ChIA-PET, promoter capture Hi-C and Hi-C data.

FLAIR (20200707)

FLAIR (Full-Length Alternative Isoform analysis of RNA) is a workflow leveraging the full-length transcript sequencing data that nanopore affords. It uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data.

focus (0.6.10)

FOCUS (Fine-mapping Of CaUsal gene Sets) is software to fine-map transcriptome-wide association study statistics at genomic risk regions. The software takes as input summary GWAS data along with eQTL weights and outputs a credible set of genes to explain observed genomic risk.

FuSeq (1.1.0)

FuSeq is a software for discovering fusion genes from paired-end RNA sequencing data. It implements a fast and accurate method to discover fusion genes based on quasi-mapping to quickly map the reads, extract initial candidates from split reads and fusion equivalence classes of mapped reads, and finally apply multiple filters and statistical tests to get the final candidates.

genometools (1.6.1)

collection of bioinformatic tools

gffcompare (0.11.8)

gffcompare can be used to compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). It can collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples) and classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).

GimmeMotifs (0.14.3)

GimmeMotifs is a pipeline for transcription factor motif analysis written in Python. It incorporates an ensemble of computational tools to predict motifs de novo from ChIP-sequencing data. Similar redundant motifs are compared using the weighted information content similarity score and clustered using an iterative procedure. A comprehensive output report is generated with several different evaluation metrics to compare and evaluate the results.

glnexus (1.2.7)

Joint variant calling for large cohort sequencing

guidance (2.02)

GUIDANCE is meant to be used for weighting, filtering or masking unreliably aligned positions in sequence alignments before subsequent analysis.

hhsuite (3.3.0)

The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

HMMER (3.3.1)

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called "profile hidden Markov models" (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models.

HTGTSrep (9fe74ff)

A pipeline for comprehensive analysis of HTGTS-Rep-seq.

igblast (1.17.0)

IgBlast is a sequence analysis tool for immunoglobulin variable domains.

ImReP (0.8)

ImReP is a novel computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data. It is able to efficiently extract TCR- and BCR-derived reads from RNA-Seq data. ImReP can also accurately assemble the complementary determining regions 3 (CDR3s), the most variable regions of B and T cell receptors, and determine their antigen specificity.

infernal (1.1.4)

Package for searching DNA sequence databases for RNA structure and sequence similarities

intarna (3.2.0)

IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules.

interproscan (5.42-78.0)

InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

InterVar (2.1.2, 2.1.3)

In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published updated standards and guidelines for the clinical interpretation of sequence variants with respect to human diseases on the basis of 28 criteria. However, variability between individual interpreters can be extensive because of reasons such as the different understandings of these guidelines and the lack of standard algorithms for implementing them, yet computational tools for semi-automated variant interpretation are not available. To address these problems, InterVar implements these criteria to help human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria.

jellyfish (2.3.0)

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

kallisto (0.46.2)

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

LASTZ (1.04.03)

LASTZ is a tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. LASTZ is a drop-in replacement for BLASTZ, and is backward compatible with BLASTZ's command-line syntax.

ldsc (3d0c4464)

ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.

m-tools (20210208)

A selection of software developed at the Australian Centre for Ecogenomics to aid in the analysis of metagenomic datasets

magma (1.06)

MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.

maps (1.1.0)

a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.

MashMap (2.0)

MashMap is an approximate algorithm for computing local alignment boundaries between long DNA sequences. Given a minimum alignment length and an identity threshold, it computes the desired alignment boundaries and identity estimates using kmer-based statistics, and maintains sufficient probabilistic guarantees on the output sensitivity.

MELT (2.2.2)

MELT is an application for identifying mobile elements in genomic data

meme (5.1.0)

MEME is used to discover motifs in groups of DNA/protein sequences or databases.

mfold (3.6)

MFOLD predicts DNA and RNA secondary structure.

MMARGE (1.0)

MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements

MoChA (1.10.2)

MoChA is a bcftools extension to call mosaic chromosomal alterations starting from phased VCF files with either B Allele Frequency (BAF) and Log R Ratio (LRR) or allelic depth (AD)

MQLS (1.5)

MQLS ("More Poweful" or "Modified" Quasi-likelihood Score Test) is a program for case-control association testing of a binary trait in samples that contain related individuals.

MUMmer (4.0.0beta2)

Mummer is a system for aligning entire genomes extremely rapidly.

MUSCLE (3.8.31)

Fast Multiple Sequence Alignment program.

mutsig2cv (3.11)

mutsig2cv analyzes somatic point mutations discovered in DNA sequencing, identifying genes mutated more often than expected by chance.

ncbi-toolkit (22.0.0)

The NCBI C++ Toolkit is a set of executables and libraries for a multitude of sequence analysis functions.

netOglyc (3.1d)

NetOglyc produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.

OligoArray (2.1.3)

OligoArray computes gene specific oligonucleotides that are free of secondary structure for genome-scale oligonucleotide microarray construction.

oncotator (

Tool for annotating information onto genomic point mutations (SNPs/SNVs) and indels.

OpenCRAVAT (1.7.0)

OpenCRAVAT is a new open source, scalable decision support system for variant and gene prioritization. It includses a modular resource catalog to maximize community and developer involvement, and as a result the catalog is being actively developed and growing every month. Resources made available via the store are well-suited for analysis of cancer, as well as Mendelian and complex diseases.

OptiType (1.3.2)

OptiType is a HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.

ORFfinder (0.4.3)

ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP.


PAINTOR (Probabilistic Annotation INtegraTOR) is a probabilistic framework that integrates association strength with genomic functional annotation data to improve accuracy in selecting plausible causal variants for functional validation.

phaser (1.1.1)

phasing and Allele Specific Expression from RNA-seq. Performs haplotype phasing using read alignments in BAM format from both DNA and RNA based assays, and provides measures of haplotypic expression for RNA based assays.

PhIP-Stat (0.3.0)

PhIP-Stat is a set of analysis tools for tools for PhIP-seq experiments. It allows for processing of PhIP-Seq raw data.

phylowgs (1.0)

This Python/C++ code is the accompanying software for the paper PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors, with authors Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, and Quaid Morris.

PRANK (150803)

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.

preseq (3.1.1)

predicting library complexity and genome coverage in high-throughput sequencing

presto (0.5.13)

pRESTO performs all stages of raw sequence processing prior to alignment against reference germline sequences.

prokka (1.14.6)

Prokka is a software tool for the rapid annotation of prokaryotic genomes.


PSIPRED is a simple and accurate secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST).

pysamstats (1.1.2)

Pysamstats is a fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

QTLtools (1.2)

A tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.

randfold (2.0)

RandFold computes the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.

regenie (20200624)

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center. regenie employs the BGEN library.

rMATS (4.1.0; 4.0.2)

MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.

rmblast (2.10.0)

RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program.

RNAmmer (1.2)

RNAmmer predicts ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models: An initial spotter model searches both strands. The spotter model is constructed from highly conserved loci within a structural alignment of known rRNA sequences. Once the spotter model detects an approximate position of a gene, flanking regions are extracted and parsed to the full model which matches the entire gene.

rnapeg (current)

RNApeg is required to generate a junctions file for use by CICERO

RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target.

rnaview (current)

The RNAView program generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.

roary (3.13.0)

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome.

rscape (1.5.2)

RNA Significant Covariation Above Phylogenetic Expectation is a program that given a multiple sequence alignment of RNA sequences

SAIGE (0.39.4)

R package for large-scale genetic association studies.

SEACR (1.0)

SEACR is intended to call peaks and enriched regions from sparse Cleavage Under Targets and Release Using Nuclease (CUT&RUN) or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).

selscan (1.3.0)

selscan is a tool for haplotype-based scans to detect natural selection, which are useful to identify recent or ongoing positive selection in genomes. It is an efficient multithreaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population EHH (XPEHH). selscan accepts phased genotypes in multiple formats, including TPED.

signalp (4.1)

SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.

smoove (0.2.5)

smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls.

SOAPdenovo-Trans is a de novo transcriptome assembler designed specifically for RNA-Seq. Its performance on transcriptome datasets from rice and mouse. It provides higher contiguity, lower redundancy and faster execution than other popular transcriptome assemblers.

sonicparanoid (1.3.5)

A stand-alone software tool for the identification of orthologous relationships among multiple species.

spacy (2.2.3)

advanced Natural Language Processing (NLP) in Python

star-seqr (0.6.7)

Star-seqr is a tool for identifying gene fusions.

steme (1.9.1)

An efficient accurate motif finder based on MEME and implemented using suffix arrays.

SurvivalGWAS_SV is an easy to use software that is able to handle large scale genome-wide data, allowing for imputed genotypes by modelling time to event outcomes under a dosage model. The software can adjust for multiple covariates and incorporate SNP-covariate interaction effects.

tantan (22)

A tool to mask low complexity and short period tandem repeats

TelomereHunter is a software for the detailed characterization of telomere maintenance mechanism footprints in the genome. The tool is implemented for the analysis of large cancer genome cohorts and provides a variety of diagnostic diagrams as well as machine-readable output for subsequent analysis.

TMHMM (2.0c)

TMHMM predicts transmembrane helices in proteins.

TRF (4.09)

A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.

unicycler (0.4.8)

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline.

usearch (11.0.667)

USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

VarScan (2.4.3)

A platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples.

VCF-kit (0.1.6; 0.2.8)

VCF-kit is a collection of utility tools for processing and analyzing the VCF (variant call format) files, including primer generation for variant validation, dendrogram production,genotype imputation from sequence data in linkage studies, and additional tools to be used by statistical and population geneticists.

viennarna (2.4.17)

RNA Secondary Structure Prediction and Comparison

viper (0-20181127-b74e0bc-p1)

VIPER combines the use of several dozen RNA-seq tools, suites, and packages to create a complete pipeline that takes RNA-seq analysis from raw sequencing data all the way through alignment, quality control, unsupervised analyses, differential expression, and downstream pathway analysis

weblogo (3.6)

contains seqlogo utility to create sequence logo summarizing sequence alignments

WISExome (20180814)

WISExome is the tool that implements a within-sample comparison approach to CNV detection. It correctly identifies known pathogenic CNVs.

xengsort (28762aac)

A fast xenograft read sorter based on space-efficient k-mer hashing.

xenome (1.0.1)

xenome is a tool for classifying reads from xenograft source.

xHLA (2018-04-04)

The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. xHLA iteratively refines the mapping results at the amino acid level to achieve high typing accuracy for both class I and II HLA genes.

back to top

CCP4 (7.1.009)

CCP4 is a suite of programs for protein crystallography and structural biology.

cryoDRGN (0.3.1)

CryoDRGN is an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It contains interactive tools to visualize a dataset’s distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions.

crystfel (0.9.1)

CrystFEL is a suite of programs for processing diffraction data acquired serially in a snapshot manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.

CSD (2020)

The Cambridge Structural Database is the world repository of small molecule crystal structures.

DeepHiC (20201001)

DeepHiC ("deep Hi-C") is a generative adversarial network aimed at predicting the high-resolution Hi-C contact maps from ithe low-coverage sequencing data. Hi-C is commonly used to study three-dimensional genome organization.

DSSP (2.2.1)

The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries. DSSP does not predict secondary structure.

emspring (0-86-1661)

SPRING (Single Particle Reconstruction from Images of kN own Geometry) is a single-particle based helical reconstruction package for electron cryo-micrographs and has been used to determine 3D structures of a variety of highly ordered and less ordered specimens.

gautomatch (0.56_cuda-9.1)

Fully automatic acccurate, convenient and extremely fast particle picking for EM

I-TASSER (5.1)

I-TASSER (Iterative Threading ASSEmbly Refinement) is a hierarchical approach to protein structure and function prediction.

lafter (1.1)

LAFTER is a local filter for single particle TEM reconstructions.

lammps (29Oct20)

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. It runs on a variety of different computer systems, including single processor systems, distributed-memory machines with MPI, and GPU and Xeon Phi systems. LAMMPS is open source software, released under the GNU General Public License.

LocScale (0.1)

LocScale is a reference-based local amplitude scaling tool using prior model information to improve contrast of cryo-EM density maps. It can be helpful in the common case of resolution variation in the 3D reconstruction and it can be used as an alternative to other commonly applied map sharpening methods.

mdtraj (1.9.4)

MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories and perform a variety of analyses, including fast RMSD, solvent accessible surface area, hydrogen bonding, etc.

moabs (1.3.2)

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing.

naccess (2.1.1)

The naccess program calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface.

pf_refinement (20Nov19)

Protofilament Refinement is a software package to further refine microtubule structures, by aligning individual protofilaments rather than full microtubule segements.

Phenix (1.19.1-4122)

PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.

PROCHECK (3.5.4)

PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.

PyMOL (2.3.0)

A comprehensive molecular visualization product for rendering and animating 3D molecular structures.

PyRosetta (268.py2.7)

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

rDock (2013.1)

The rDock platform is a suite of command-line tools for high-throughput docking and virtual screening.

Schrodinger (2020.4)

A limited number of Schrödinger applications are available on the Biowulf cluster through the Molecular Modeling Interest Group. Most are available through the Maestro GUI.

Scipion (3.0.6)

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

scratch1d (1.3)

SCRATCH-1D is a suite of one-dimensional predictors included in the long-established and widely used SCRATCH suite of predictors developed by the Institute for Genomics and Bioinformatics (IGB) of the University of California, Irvine (UCI).

Sidesplitter reduces over-fitting in both idealised and experimental settings, while maintaining independence between the two sides of a split refinement. It can improve the final resolution in refinements of structures prone to severe over-fitting, such as membrane proteins in detergent micelles.

VMD (1.9.3)

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. To use, type vmd at the prompt.

Xplor-NIH (2.52)

Xplor-NIH is a structure determination program which builds on the X-PLOR v3.851 program, including additional tools developed at the NIH.

ZDOCK (3.0.2)

ZDOCK predicts protein-docking models, and uses a fast Fourier transform to search all possible binding modes for proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics.

back to top

AMON (1.0.0)

AMON (Annotation of Metabolite Origins via Networks) is an open-source bioinformatics application that can be used to (1) annotate which compounds in the metabolome could have been produced by bacteria present or the host; (2) evaluate the pathway enrichment of host verses microbial metabolites, and (3) to visualize which compounds may have been produced by host versus microbial enzymes in KEGG pathway maps.

cellphonedb (2.1.4)

A publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately.

eggNOGmapper (1.0.3)

eggNOGmapper is a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database. Orthology assignment is ideally suited for functional inference. However, predicting orthology is computationally intensive at large scale, and most other pipelines are relatively inaccessible (e.g., new assignments only available through database updates), so less precise homology-based functional transfer was previously the default for (meta-)genome annotation.

EukRep (20180308)

Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, eukaryotic genomes shoould be recovered from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. EukRep is a kmer- and SVM-based strategy for eukaryotic sequence identification from environmental samples.

genesis (2.4)

GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.

GRNBoost (20191216)

GRNBoost is a library built on top of Apache Spark that implements a scalable strategy for gene regulatory network (GRN) inference. GRNBoost was inspired by GENIE3, a popular algorithm for GRN inference. GRNBoost adopts GENIE3's algorithmic blueprint and aims at improving its runtime performance and data size capability.

MAKER (2.31.10)

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

Neuron (7.6.5)

NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties.

vdjtools (1.2.1)

A comprehensive analysis framework for T-cell and B-cell repertoire sequencing data.

back to top

aria2 (1.33.1)

multiprotocol download utility
Type 'module load aria2'then 'aria2c --help' for more info.

ariba (2.14.4)

Antimicrobial resistance identification.

asciinema (2.0.1)

asciinema [as-kee-nuh-muh] is a free and open source solution for recording terminal sessions and sharing them.
Type 'module load asciinema' then 'asciinema' to run.

Aspera (3.7..4)

High-speed fasp-powered file transfers. Mostly used to download data from NCBI, which has an Aspera server. See the data transfer page for details.

AWS (1.16.263)

Command-line tools for Amazon Web Services. Use 'module load python; aws -help' to see the command-line help, or

bbcp (

Secure and fast copy utility

bgionline (2.2.15)

BGI Online is a cloud platform for bioinformatic analysis. The BGI online tools can be used for downloading data and more. Use 'module load bgionline' to access the tools. [Documentation]

chance (1.0)

CHANCE performs CHiP-seq analytics and confidence estimation.

circos (0.69-9)

Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. Also, Circos is useful to visualize any type of information that benefits from a circular layout. Thus, although it has been designed for the field of genomics, it is sufficiently flexible to be used in other data domains.

coreutils (8.31)

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system.

cpdf (2.3.1)

Coherent PDF tools

crumble (0.8.3)

Crumble is a tool to explore controlled loss of quality values for compressing CRAM files. Crumble can read a SAM/BAM/CRAM file, compute which confidence values to keep and which to omit, and emit a new file with most qualities removed.

cryolo (1.5.3)

Automated particle picker for cryo-EM

datalad (0.13.0rc2)

Datalad is a tool for uploading and downloading public up-t-to-date neuroimaging datasets.

datamash (1.7)

GNU datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files.

EDirect (14.5)

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.

Text Editors available on the systems

gdc-client (1.5.0)

The GDC Data Transfer Tool provides an optimized method of transferring data to and from the GDC, and enables resumption of interrupted transfers.

gdrive (2.1.0)

gdrive is a command line utility for interacting with Google Drive.

gen3-client (2020.05)

The gen3-client provides an easy-to-use, command-line interface for uploading and downloading data files to and from a Gen3 data commons from the terminal or command prompt.

Ghostscript (9.22)

Ghostscript is an interpreter for the PostScript language and for PDF.

gnuplot (5.4.0)

Gnuplot is a portable command-line driven graphing utility to visualize mathematical functions and data interactively, and can support many non-interactive uses such as web scripting.
Type 'gnuplot' to run, or 'module avail gnuplot' to see other available versions.

google-cloud-sdk (289.0.0)

Google Cloud SDK is a set of tools that you can use to manage resources and applications hosted on Google Cloud Platform. These include the gcloud, gsutil, and bq command line tools. See docs at
Type 'module load google-cloud-sdk' to use on Biowulf.

Grace (5.1.25)

Grace is a WYSIWYG 2D plotting tool for the X-Window system. It is a successor to Xmgr.
Type 'module load grace', then 'xmgrace' or 'gracebat' to run.

graphviz (2.40)

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

groff (1.22.3)

Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. Output may be PostScript or PDF, html, or ASCII/UTF8 for display at the terminal. Formatting commands may be either low-level typesetting requests (“primitives”) or macros from a supplied set. Users may also write their own macros. All three may be combined.

gzip (1.9)

the data compression program

h5utils (1.13.1)

h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format. Type 'module load h5utils' to access the executables (e.g. h5topng)

ImageMagick (7.0.7)

ImageMagick is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats.
The ImageMagick tools are available by default (e.g. type 'convert') or use 'module load ImageMagick' to load the latest versions.

jo (1.1)

A small utility to create JSON objects from command line arguments.

jq (1.5)

Command line json processor

kronatools (2.7)

Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser.

lbzip2 (2.5)

lbzip2 is a multi-threaded compression utility with support for bzip2 compressed file format.

longshot (0.3.5)

Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).

mc (4.8.22)

GNU Midnight Commander is a visual file manager, with a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Type module load mc and then the command mc to get started.

mercurial (4.5.3)

mercurial is a version control system that runs within Python. To use, type ml python/2.7. For help, type hg --help.

MySQL (8.0.22)

MySQL is an open-source relational database management system.

neovim (0.4.4)

Neovim is a refactor, and sometimes redactor, in the tradition of Vim (which itself derives from Stevie). It is not a rewrite but a continuation and extension of Vim.

netpbm (10.86.17)

Netpbm is a toolkit for manipulation of graphic images, including conversion of images between a variety of different formats. There are over 300 separate tools in the package including converters for about 100 graphics formats. Examples of the sort of image manipulation we're talking about are: Shrinking an image by 10%; Cutting the top half off of an image; Making a mirror image; Creating a sequence of images that fade from one image to another.

nvchecker (1.7)

nvchecker (short for new version checker) is for checking if a new version of some software has been released.

parallel (20210222)

GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

paraview (5.8.1)

ParaView is an open-source, multi-platform data analysis and visualization application.

patchelf (0.12)

patchelf is a small utility to modify the dynamic linker and RPATH of ELF executables.

pdf2svg (0.2.3)

A simple PDF to SVG converter using the Poppler and Cairo libraries.

pigz (2.4)

pigz (parallel implementation of gzip) is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.

pilon (1.23)

Pilon is a software tool which can be used to: 1) Automatically improve draft assemblies 2) Find variation among strains, including large event detection

POVRay (3.7)

POVRAY (Persistence of Vision RAYtracer) is a high-quality tool for creating three-dimensional graphics. Raytraced images are publication-quality and 'photo-realistic', but are computationally expensive so that large images can take many hours to create.

pysurfer (0.9.0)

PySurfer is a Python library for visualizing brain surfaces produced by neuroimaging datasets.

rclone (1.53.1)

Rclone is a utility for synchronizing directories on a file-based storage system (e.g. /home or /data) with an object store such as Amazon S3. It uses the S3 protocol, and it can be used with the HPC object storage system.

rdfind (1.4.1)

rdfind is a program that finds duplicate files. It is useful for compressing backup directories or just finding duplicate files. It compares files based on their content, NOT on their file names. After typing module load rdfind, type man rdfind for more information.

rfmix (2.0)

Local Ancestry and Admixture Inference

rnaview (current)

The RNAView program generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.

screen (4.8.0)

Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells.

singularity (3.7.1)

Singularity is a container platform focused on supporting ``Mobility of Compute``. It allows users to emulate, and share custom Linux environments allowing for the creation of self-contained development stacks.

snp-sites (2.4.1)

Rapidly extracts SNPs from a multi-FASTA alignment

spark (2.4.0)

Apache Spark is a fast and general engine for large-scale data processing. It is commonly used as an in-memory alternative to Hadoop MapReduce.

SQLite (3.34.1)

SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.

stow (2.2.2)

GNU Stow is a symlink farm manager which takes distinct packages of software and/or data located in separate directories on the filesystem, and makes them appear to be installed in the same place.

Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.

synapseclient (1.9.1)

The synapseclient package provides an interface to Synapse, a collaborative workspace for reproducible, data intensive research projects

sysbench (1.0.20)

sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server.

TAU (2.27)

TAU - an acronym for Tuning And Analysis Utilities - is a suite of software tools for measuring performance of software packages running on a High Performance Computing resource such as the Biowulf cluster. It has the capability to measure CPU, memory, and I/O performance throughout the execution of an application.

texinfo (6.6)

Texinfo is the official documentation format of the GNU project

tmux (2.9)

tmux is a terminal multiplexer.
Type 'module load tmux' to load the module, then 'tmux --help'

UK Biobank tools for downloading and processing UKBB data. Type 'module load ukbb' to access them.

uropa (3.5.0)

UROPA is a command line based tool for genomic region annotation

vartrix (1.1.4)

VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.

vcf2db (2020.09.14)

vcf2db creates a gemini-compatible database from a VCF.

visidata (2.2)

VisiData is an interactive multitool for tabular data

whatshap (0.18)

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

wuzz (0.4.0)

Interactive cli tool for HTTP inspection

xclip (0.13)

xclip is a command line utility that is designed to run on any system with an X11 implementation. It provides an interface to X selections ("the clipboard") from the command line. It can read data from standard in or a file and place it in an X selection for pasting into other X applications. xclip can also print an X selection to standard out, which can then be redirected to a file or another program.

xpdf (4.02)

Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source.

back to top

cromwell (57)

A Workflow Management System geared towards scientific workflows.

nextflow (20.10.0)

Data-driven computational pipelines

snakemake (5.24.1)

Snakemake aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. It is well suited for bioinformatic workflows.