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.

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Acemd (3212u1)

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 (18)

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

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 (c39b2)

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

GAMESS (30Sep18-R3-sockets)

GAMESS is a general ab initio quantum chemistry package.

Gaussian (G16-A03)

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

Gromacs (2018.3+plumed2.5b)

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 (2.12)

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 on both Helix and Biowulf.

NWChem (6.6)

NWChem is an open source computational chemistry package that includes scalable tools for both classical and ab initio molecular simulations.

Psi4 (1.1)

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 (2018.1)

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.

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Basset (0.1.0)

Deep convolutional neural networks for DNA sequence analysis.

Caffe2 (0.8.1)

Caffe2 aims to provide an easy and straightforward way for you to experiment with deep learning and leverage community contributions of new models and algorithms. You can bring your creations to scale using the power of GPUs in the cloud or to the masses on mobile with Caffe2's cross-platform libraries.

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.

cuDNN (5.0.5)

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 (20180828)

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

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.

DEXTR-PyTorch (20180710)

DEXTR-PyTorch implements a new approach (Deep Extreme Cut) to image labeling where extreme points in an object (left-most, right-most, top, bottom pixels) are used as input to obtain precise object segmentation for images and videos. This is done by adding an extra channel to the image in the input of a convolutional neural network (CNN), which contains a Gaussian centered in each of the extreme points. The CNN learns to transform this information into a segmentation of an object that matches those extreme points.

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.

Few-Shot-ssl (20180723)

Few-Shot semi-supervised learning (few-short-ssl) package implements learning algorithms that specifically allow for better generalization on problems with small labeled training sets.

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.

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 (0.1.3)

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.

U-Net (20180704)

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.

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abruijn (1.0)

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

abyss (2.0.3)

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.

AfterQC (0.9.6)

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

albacore (2.3.3)

ONT basecaller

AMOS (3.1.0)

ANNOgesic (0.7.18)

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.

AnnotSV (1.1.1)

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 (2018-04-16)

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

ascatNgs (4.2.1)

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

asciigenome (1.13.0)

ASCIIGenome is a text-only command line genome browser.

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.

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 (http://samtools.sourceforge.net). 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 is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format.

bamreadcount (0.8.0)

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

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

bbtools (38.06)

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 (1.0.9)

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

bcl2fastq (2.20.0)

a tool to handle bcl conversion and demultiplexing

bedops (2.4.35)

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 (2.27.1)

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.

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.

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.

biom-format (2.1.5)

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

bismark (0.20.0)

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 (1.2.2)

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

bowtie2 (2.3.4)

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 (6.1.2)

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 (0.33.0)

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 (3.0.2)

BUSCO completeness assessments employ sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB (www.orthodb.org) 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.

Canu (1.7)

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 (1.38)

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.

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.

cellranger (3.0.0)

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

cgpBattenberg (3.3.0)

Detect subclonality and copy number in matched NGS data

ChromHMM (1.15)

ChromHMM is software for learning and characterizing chromatin states.

circleseq (1.0)

Circleseq takes sample-specific paired end FASTQ files as input and produces a list of CIRCLE-seq detected off-target cleavage sites as output.

circos (0.69-6)

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.

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 (0.9.3)

Copy number variant detection from targeted DNA sequencing

cnvnator (0.3.3)

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

conpair (10102016)

Concordance and contamination estimator for tumor–normal pairs

CONTRA (2.0.8)

CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

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 (1.0.5)

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

crossmap (0.2.6)

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 (1.0.3)

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

ctk (1.1.2)

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 (1.18)

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

deeptools (3.1.3)

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

deepvariant (0.7.0)

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 (0.7.9)

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 (1.11)

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.

discovar (52488)

DISCOVAR is a new genome assembler and variant caller for state-of-the-art data. Currently it takes as input Illumina reads of length 250 or longer -- produced on MiSeq or HiSeq 2500 -- and from a single PCR-free library.

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

drompa (3.5.0)

Peak-calling, Visualization, Normalization and QC for ChIP-seq analysis

dropseq (1.12)

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

drseq (2.0.2)

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.

eager (1.92)

EAGER: efficient ancient genome reconstruction

edd (1.1.19)

EDD is a ChIP-seq peak caller for detection of megabase domains of enrichment.

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.

EricScript (0.5.5)

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

exceRpt (4.4.0)

The extra-cellular RNA processing toolkit (exceRpt) was designed to handle the variable contamination and often poor quality data obtained from low input smallRNA-seq samples such as those obtained from extra-cellular preparations. However the tool is perfectly capable of processing data from more standard cellular preparations and, with minor modifications to the command-line call, is also capable of processing WGS/exome and long RNA-seq data.

exomiser (10.0.1)

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 (0.11.8)

It provide quality control functions to next gen sequencing data.

fastqtools (0.8)

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

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 (1.0.0)

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 (http://www.hsph.harvard.edu/alkes-price/software/) and shellfish (https://github.com/dandavison/shellfish). FlashPCA is based on the https://github.com/yixuan/spectra/ 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 (2.3.6)

Fast and accurate de novo assembler for single molecule sequencing reads

fqtools (2.0)

Tools for manipulating fastq files

freec (11.5)

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 (4.0.11.0)

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.

gdc-client (1.3.0)

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

gem (3.0)

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

Gemini (0.20.1)

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 (0.96)

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 at Helix Systems is a mirror of the UCSC Genome Browser. The URL is https://hpcnihapps.cit.nih.gov/genome. Users can also access the MySQL databases, supporting files directly, and a huge number of associated executables.

genomestrip (2.00.1833)

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.

Gistic (2.0.23)

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

gmap-gsnap (2017-09-05)

A Genomic Mapping and Alignment Programs

gossamer (ac492a8 )

A tool for de novo assembly of high throughput sequencing data.

graphmap (0.5.2)

A highly sensitive and accurate mapper for long, error-prone reads

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.

Hail (0.2.3)

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

hap.py (0.3.7)

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

hgvs (1.2.4)

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.

hichipper (0.7.3)

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 (2.10.0)

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

hisat (2.0.5)

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

HLA-PRG-LA (0.85.45c4fea)

Stands for HLA PRG, linear approximation. The basic idea is to seed graph alignments with linear alignments to the sequences that the graph consists of.

homer (4.10.1)

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

htgts (v2)

High-Throughput Genome-Wide Translocation Sequencing pipeline

htseq (0.9.1)

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

humann2 (0.11.1)

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).

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.

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 (2.4.14)

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

IGVTools (2.4.14)

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 (2.0)

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 (02.16.03.09)

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 (1.0.3)

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.

JAMM (1.0.7.1)

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 (1.5.6)

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

kaiju (1.6.2)

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.

KMC (3.0.0)

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 (2.0.7-beta)

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

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 (1.0.7)

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 (2.1.3.1)

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 (2.1.1.20160309)

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 (7.407)

Multiple alignment program for amino acid or nucleotide sequences

MAGeCK (0.5.7)

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.

magicblast (1.4.0)

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 (1.0.5)

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 (1.2.0)

Structural variant and indel caller for mapped sequencing data

mapsplice (2.1.8)

Accurate mapping of RNA-seq reads for splice junction discovery

mash (2.0)

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

megahit (1.1.4)

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 contstruction.

MEGAN (6.12.1)

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.

metal (2017-12-21)

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 (2.7.8)

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 (0.5.3)

fast and accurate alignment tool for PacBio and Nanopore long reads

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 (2.13)

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 (2.0.0.8)

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

mirge (2.0.5)

A microRNA sequencing analysis tool.

miso (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 (2.1.10)

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

mosdepth (0.2.3)

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 (1.6)

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.

MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.

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.

neusomatic (0.1.1)

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.

ngsqctoolkit (2.3.3)

A toolkit for the quality control (QC) of next generation sequencing (NGS) data.

NGSutils (0.5.9)

NGSUtils is a suite of software tools for working with next-generation sequencing datasets.

nirvana (2.0.4)

Nirvana provides clinical-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, and SVs (including CNVs). It can be run as a stand-alone package or integrated into larger software tools that require variant annotation.

novocraft (3.09.01)

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.

oases (0.2.09)

oases is a de novo transcriptome assembler based on the Velvet genome assembler core.

parpipe (79b1aab)

Complete analysis pipeline for PAR-CLIP data

PartekFlow (7.0.18.0218)

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

PASApipeline

PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data.

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 (0.3.1)

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 (2.17.11)

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 (1.1.0)

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

pindel (0.2.5b8)

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.

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 (1.9.0-beta4.4)

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

porechop (0.2.3)

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 (2.0.3)

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.

probabel (0.4.3)

ProbABEL is a Tool for genome-wide association analysis of imputed genetic data. It was designed to perform such regression in fast, memory-efficient and consequently genome-wide feasible manner. Currently, ProbABEL implements linear, logistic regression, and Cox proportional hazards models.

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 (0~20180710.f4fd019)

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

pvactools (1.1.4)

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

pyclone (0.13.1)

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

pyDNase (0.2.6)

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

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.

RapMap (0.5.0)

RapMap is a tool for rapid sensitive and accurate read mapping via quasi-mapping. It is capable of mapping sequencing reads to a target transcriptome substantially faster than existing alignment tools.

Rcorrector (1.0.3.1)

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 (0.4.5)

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

RepeatMasker (4.0.7)

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.

rgt (0.11.3)

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

rilseq (0.60)

RILseq computational protocol

rmats (4.0.2)

MATS is a computational tool to detect differential alternative splicing events from 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 (1.3.0 )

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

rseqc (2.6.4)

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

rvtests (20171010 or 2.0.6)

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 (0.11.3)

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

sambamba (0.6.7)

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 (1.9)

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

scallop (0.10.2)

Scallop is a reference-based transcript assembler.

scalpel (0.5.3)

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 (1.3.2)

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

segemehl (0.2.0)

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

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 (1.2-r94)

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-ICE (20170728)

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

shapeit (2.r904)

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 (1.1)

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 (0.3.3)

SLAMseq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. 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.

smrtanalysis (6.0.0.47841)

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.

sniffles (1.0.10)

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.

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 (4.3t)

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 (1.0.5.0)

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.

spades (3.13.0)

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

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 (2.9.1)

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

stampy (1.0.32)

Short read aligner

STAR (2.6.1c)

Spliced Transcripts Alignment to a Reference

STAR-Fusion (1.5.0)

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 (2.7.1)

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

stringtie (1.3.4)

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.

subread (1.6.3)

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.

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.

sv2 (1.4.3.4)

Support Vector Structural Variation Genotyper

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.

SVPV (1.01)

SVPV (Structural Variant Prediction Viewer) enables visualisation of predicted structural variant regions in paired-end whole genome sequencing alignments, and allows comparison of calls from differenct structural variant prediction algorithms.

svtyper (0.1.4)

Svtyper is a Bayesian genotyper for structural variants.

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.

telseq (0.0.1)

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

tetoolkit (2.0.3)

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.

TransDecoder (5.0.1)

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.

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 (0.4.5)

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

trimmomatic (0.36)

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

trinity (2.8.4)

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.

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

TVC (5.8.0)

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

umitools (0.5.3)

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

vcf2maf (1.6.16)

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

vcfanno (0.2.9)

annotate a VCF with other VCFs/BEDs/tabixed files

vcflib (v1.0.0-rc0-279-gc71853a)

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

vcftools (0.1.15)

VCFtools contains a Perl API (Vcf.pm) 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 (94)

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.

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

vsearch (2.8.1)

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 (0.577)

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.

zUMIs (0.0.6)

zUMIs is a fast and flexible pipeline to process RNA-seq data with UMIs.

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3DSlicer (4.10.0)

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 (2.3.1)

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.

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.

Caret (5.65)

Caret is a free, open-source, software package for structural and functional analyses of the cerebral and cerebellar cortex. It is largely deprecated by the Connectome Workbench but is needed for the full functionality of that program.

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 (4.1.10)

Programs for finding CTFs of electron micrographs

dcm2niix (1.0.20180622)

DICOM to NIfTI converter

elastix (4.9)

a toolbox for rigid and nonrigid registration of images.

EMAN2 (2.22)

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

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.

fmriprep (1.2.5)

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.

frealix (1.1.0)

Frealix is a program for the refinement of helical filament reconstructions from cryo electron micrographs. It is primarily used to process images of amyloid fibrils, though it has also been tested on TMV and actin filaments.

Freesurfer (6.0.0)

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 (6.0.0)

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 (18.10.0-p1)

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 (4.0.1)

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

minc-toolkit (1.9.16)

This metaproject bundles multiple MINC-based packages that historically have been developed somewhat independently

MIPAV (7.2.0)

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 (1.1.0)

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 (0.14.2)

MRIQC is an MRI quality control tool

mrtrix (3.0_RC3)

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.

PEET (1-10-1)

PEET (Particle Estimation for Electron Tomography) is an open-source package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. It seeks the optimal alignment of each particle against a reference volume through several iterations. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD.

RELION (2.1.0)

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 (2.1.0)

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).

situs (2.8)

Situs is a package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

summovie (1.0.2)

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

TeraStitcher (1.10.12)

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.

TORTOISE (3.1.3)

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

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.

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AdmixTools (4.1)

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 (3.1)

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 (5.0_28Sep18)

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.

BEAST (1.10.2,2.5.1)

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 (6.1.4)

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.

freebayes (1.2.0)

Bayesian haplotype-based polymorphism discovery and genotyping

GCTA (1.91.6beta)

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.

integrative (20180522)

Software Pipeline for Integrative Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization

king (2.1.4)

Quick Links Documentation Notes Interactive job Batch job Swarm of jobs 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.

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 (5.0.0)

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

Mendel (16.0)

Mendel is a comprehensive package for exact statistical genetic analysis of qualitative and quantitative traits.

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 (1.40.5)

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

mr-mega (0.1.5)

Meta-Regression of Multi-Ethnic Genetic Association

Pascal (2016-01-25)

Pascal (Pathway scoring algorithm) is a program for calculating gene score and pathway score p-values from GWAS-summary statistics.

pedcut (1.19)

A program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size

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.

prest (3.02)

PREST is a program that detects pedigree errors by use of genome-screen data.

PRSice (2.1.3.beta)

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

QIIME (2-2018.8)

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 (8.2.11)

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML).

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 (2.r904)

SHAPEIT is a fast and accurate haplotype inference software

SMR (0.702)

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 is a program for multipoint, oligogenic, variance component linkage analysis in pedigrees of arbitrary size and complexity (Almasy L; Blangero J, 1998).

treemix (1.12)

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

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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 https://biospec.nih.gov, or by using the Mascot daemon on your own desktop PC.

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ANTs (2.3.1)

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

Comsol (54)

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.

IDL/ENVI (8.5/5.3)

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.

Mathematica (11.3)

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

Matlab (2018b)

MATLAB is a high-performance 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.

Meep (1.4.3)

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 (4.4.0)

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.

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 (3.4,3.5)

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 (1.1.447)

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 (9.4)

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

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Chimera (1.12.0)

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 (0.8.9)

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

Cytoscape (3.6.0)

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.

lammps (16Mar18)

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.

lancet (1.0.7)

Lancet is a somatic variant caller (SNVs and indels) for short read data.

OpenBabel (2.4.1)

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

Psi4 (1.1)

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

Quantum Espresso (QE) is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The Quantum Espresso distribution contains the core packages PWscf (Plane-Wave Self-Consistent Field) and CP (Car-Parrinello) for the calculation of electronic-structure properties within Density-Functional Theory (DFT), using a Plane-Wave (PW) basis set and pseudopotentials.

Rosetta (2018.42)

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 (2018.1)

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.

TINKER (8.4.3)

TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber, CHARMM, Allinger MM, OPLS, Merck Molecular Force Field, Liam Dang's polarizable model, and the AMOEBA polarizable atomic multipole force field.

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.

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Accurity (20180724)

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

ACFS (20180316)

ACFS is an Accurate CircRNA Finder Suite for discovering circRNAs from RNA-Seq data. CircRNAs are generated through splicing, or to be precise, back-splicing where the downstream splice donor attacks an upstream splice acceptor. Identifying the exact site of back-splice lies in the heart of circRNA discovery. No prior knowledge of gene annotation is needed for circRNA prediection. ACFS is designed for Single-end RNA-Seq reads. Paired-end data is also supported, albeit with lower sensitivity.

alleleCount (3.3.1)

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.

Azimuth (2.0)

Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency.

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.

Blast (2.8.0+alpha)

NCBI's famous 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 (2.3.2)

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

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

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)

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.

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.

diamond (0.9.9)

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 https://hpcwebapps.cit.nih.gov/dnaworks/.

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 (2.2.0)

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.

genometools (1.5.9)

collection of bioinformatic tools

gffcompare (0.10.5)

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).

hhsuite (3.0-beta.3)

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 (3.1b2)

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.

IgBlast (1.7.0)

IgBlast is a sequence analysis tool for immunoglobulin variable domains.

interproscan (5.29-68.0)

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 (2.0)

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 (2.2.10)

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

kallisto (0.44.0)

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.

khmer (2.1.2)

Library and suite of command line tools for working with short-read, DNA sequences, taking a k-mer-centric approach to sequence analysis.

LASTZ (1.04.00)

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 (1.0.0-101-g89c13a7)

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

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.

meme (4.12.0)

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

mfold (3.6)

MFOLD predicts DNA and RNA secondary structure.

MUMmer (4.0.0beta2)

Mummer is a system for aligning entire genomes extremely rapidly.

MUSCLE (3.8.31)

Fast Multiple Sequence Alignment program.

ncbi-toolkit (21.0.0)

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

OligoArray (2.1)

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

oncotator (1.9.1.0)

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

ORFfinder (0.4.0)

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.

Oyster River Protocol (ORP) implements a standardized and benchmarked set of bioinformatic processes, resulting in a transcriptome assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multiassembler and kmer assembly process, thereby bypassing the shortcomings i of any one approach.

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.

presto (0.5.7)

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

prokka (1.13)

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

PSIPRED (4.0)

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).

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.

rmblast (2.6.0.2)

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.

roary (3.12.0)

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.

smoove (0.2.1)

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.

steme (1.9.1)

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

tantan (13)

A tool to mask low complexity and short period tandem repeats

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.

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)

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 (2.4.4)

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.

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.

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CCP4 (7.0.066)

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

crystfel (0.7.0)

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 (5.39)

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

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)

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.

lammps (16Mar18)

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.

mdtraj (1.9.1)

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.

NWChem (6.6)

NWChem is an open source computational chemistry package that includes scalable tools for both classical and ab initio molecular simulations.

osprey (2.2~beta)

OSPREY is a suite of programs for computational structure-based protein design. OSPREY is specifically designed to identify protein mutants that possess desired target properties (e.g., improved stability, switch of substrate specificity, etc.). OSPREY can also be used for predicting small-molecule drug inhibitors and for designing protein-protein and protein-peptide interactions.

Phenix (1.13-2998)

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 (2.1.0)

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

PyRosetta (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.

raptorx (37223)

RaptorX is a protein structure prediction server developed by Xu group, excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions.

rDock (2013.1)

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

Schrodinger (2018.1)

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 (1.2)

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.

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 (2.46)

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

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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.

Neuron (7.5)

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 (1.1.10)

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

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aria2 (1.33.1)

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

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 (Jul2015)

Command-line tools for Amazon Web Services. Use 'module load python; aws -help' to see the command-line help, or http://aws.amazon.com/cli/.

bbcp (15.02.03.01.1)

Secure and fast copy utility

bgionline (0.1)

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]

coreutils (8.27)

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

Coherent PDF tools

EDirect (10.0)

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

Ghostscript (9.22)

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

gnuplot (5.2.2)

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 (221.0.0)

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 https://cloud.google.com/sdk/docs/how-to.
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.

mc (4.8.19)

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 (4.5.0)

mercurial is a version control system that runs within Python.

MySQL (5.5.54)

MySQL is an open-source relational database management system.

niftilib (2.0.0)

Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images.

parallel (20171222)

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

paraview (5.4.1)

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

patchelf (0.9)

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

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.

rdfind (1.3.5)

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.

singularity (3.0.1-20181121-a50b5b35)

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.

Spark (2.1.1)

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 (3.22.0)

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 (1.9.0)

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

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.

tmux (2.6)

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.

vartrix (1.1.0)

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

vcf2db (2018.10.26)

vcf2db creates a gemini-compatible database from a VCF.

wuzz (0.4.0)

Interactive cli tool for HTTP inspection

xpdf (4.00)

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.

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cromwell (34)

A Workflow Management System geared towards scientific workflows.

nextflow (0.30.2)

Data-driven computational pipelines

snakemake (5.3.0)

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.