Application updates in the last 3 months
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Updated Application
4 Mar 2024 pyem updated to version 240209
UCSF pyem is a collection of Python modules and command-line utilities for electron microscopy of biological samples.
4 Mar 2024 mc updated to version 4.8.31
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.
4 Mar 2024 autoconf updated to version 2.72
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.
4 Mar 2024 gnuplot updated to version 6.0.0
Gnuplot is a portable command-line driven graphing utility to visualize mathematical functions and data interactively, and can support many non-interactive uses such as web scripting.
Type 'gnuplot' to run, or 'module avail gnuplot' to see other available versions.
3 Mar 2024 nodejs updated to version 20.11.1
Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs
3 Mar 2024 RepeatMasker updated to version 4.1.6
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.
1 Mar 2024 model-angelo updated to version 1.0.11
ModelAngelo is an automatic atomic model building program for cryo-EM maps.
1 Mar 2024 tortoisev4 updated to version current
TORTOISE (Tolerably Obsessive registration and Tensor Optimization Indolent Software Ensemble) is a suite of programs for for pre-processing, post-processing and analyzing diffusion MRI data
29 Feb 2024 mpich updated to version 4.1.3
MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2).
29 Feb 2024 boost updated to version 1.84
Boost provides free peer-reviewed portable C++ source libraries. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
29 Feb 2024 Julia updated to version 1.10.1
high level, dynamic language for technical computing
28 Feb 2024 quarto updated to version 1.4.550
Quarto is an open-source scientific and technical publishing system built on Pandoc
28 Feb 2024 parallel updated to version 20240222
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
28 Feb 2024 lazygit updated to version 0.40.2
A simple terminal UI for git commands
28 Feb 2024 SignatureAnalyzer updated to version 20240208
SignatureAnalyzer is a tool for the identification of somatic mutational signatures. It employs Bayesian non-negative matrix factorization (NMF).
26 Feb 2024 slapnap updated to version 20210507
The slapnap container is a tool for using the Compile, Analyze and Tally NAb Panels (CATNAP; Yoon et al. 2015) database to develop predictive models of HIV-1 neutralization sensitivity to one or several broadly neutralizing antibodies (bnAbs).
26 Feb 2024 pySCENIC updated to version 0.12.1
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering). It enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
26 Feb 2024 glog updated to version 0.7.0
The glog library implements application-level logging. This library provides logging APIs based on C++-style streams and various helper macros.
26 Feb 2024 JAX-CNV updated to version 20240208
JAX-CNV implemens an algorithm for copy number variant (CNV) calling from the whole-genome sequencing (WGS) data. On testing data, it demonstrated ~7-fold increase in the number of detected CNVs as compared to the chromosomal microarray assay (CMA) for clinical diagnosis.
21 Feb 2024 NucleoATAC updated to version 0.3.4
NucleoATAC is a software for nucleosome calling using ATAC-seq. It can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy.
20 Feb 2024 famsa updated to version 2.2.2
Progressive algorithm for large-scale multiple sequence alignments
16 Feb 2024 rust updated to version 1.76.0
A language empowering everyone to build reliable and efficient software.
15 Feb 2024 fastqc updated to version 0.12.1
It provide quality control functions to next gen sequencing data.
15 Feb 2024 bamreadcount updated to version 1.0.1
Bam-readcount generates metrics at single nucleotide positions. There are number of metrics generated which can be useful for filtering out false positive calls.
15 Feb 2024 synapseclient updated to version 4.0.0
The synapseclient package provides an interface to Synapse, a collaborative workspace for reproducible, data intensive research projects
15 Feb 2024 percolator updated to version rel-3-06-05
A software for postprocessing of shotgun proteomics data
14 Feb 2024 nda-tools updated to version 0.2.12,0.2.16,0.2.26
In order to submit data to the National Institute of Mental Health Data Archives (NDA), users must validate their data to ensure it complies with the required format. This is done using the NDA validation tool, vtcmd. Additionally, users can package and download data from NDA as well, using the downloadcmd tool.
13 Feb 2024 sambamba updated to version 1.0.1
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.
13 Feb 2024 multiqc updated to version 1.20
aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report
13 Feb 2024 bedtools updated to version 2.31.1
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.
13 Feb 2024 seqkit updated to version 2.7.0
A cross-platform toolkit for FASTA/Q file manipulation
11 Feb 2024 trgt updated to version 0.8.0
TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat. TRGT comes with a companion tool TRVZ for visualization of reads overlapping the repeats.
8 Feb 2024 GATK updated to version 4.5.0.0
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.
8 Feb 2024 TensorQTL updated to version 1.0.9
ensoorQTL leverages general-purpose libraries and graphics processing units (GPUs) to achieve high efficiency of computations at low costR. Using PyTorch or TensorFlow it allows > 200-fold decreases in runtime and ~ 5–10-fold reductions in cost when running on GPUs relative to CPUs.
7 Feb 2024 HMMER updated to version 3.4
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.
7 Feb 2024 crossmap updated to version 0.7.0
CrossMap is a program for convenient conversion of genome coordinates between different assemblies (e.g. mm9->mm10). It can convert SAM, BAM, bed, GTF, GFF, wig/bigWig, and VCF files
7 Feb 2024 biom-format updated to version 2.1.15
tool (and library) to manipulate Biological Observation Matrix (BIOM) Format files
7 Feb 2024 bbtools updated to version 39.06
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.
7 Feb 2024 asciinema updated to version 2.4.0
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.
6 Feb 2024 rstudio-server updated to version 2023.06.0-421
RStudio Server is a web-based R IDE similar to RStudio Desktop.
5 Feb 2024 netmhcpan updated to version 4.1
netMHCpan predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks
5 Feb 2024 lefse updated to version 1.1.2
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.
5 Feb 2024 philosopher updated to version 5.1.0
Philosopher is fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery.
4 Feb 2024 chopper updated to version 0.7.0
Filtering and trimming for long-read sequencing data (PacBio/ONT).
3 Feb 2024 meme updated to version 5.5.5
MEME is used to discover motifs in groups of DNA/protein sequences or databases.
1 Feb 2024 amr updated to version 3.11.26
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
29 Jan 2024 vatools updated to version 5.1.0
VAtools is a python package that includes several tools to annotate VCF files with data from other tools.
29 Jan 2024 ANNOgesic updated to version 1.0.22; 1.1.14
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.
29 Jan 2024 ImReP updated to version 0.8
ImReP is a novel computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data. It is able to efficiently extract TCR- and BCR-derived reads from RNA-Seq data. ImReP can also accurately assemble the complementary determining regions 3 (CDR3s), the most variable regions of B and T cell receptors, and determine their antigen specificity.
27 Jan 2024 deepvariant updated to version 1.6.0
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
26 Jan 2024 AlphaPulldown updated to version 1.0.4
AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command-line interface, a variety of confidence scores and a graphical analysis tool.
26 Jan 2024 EDirect updated to version 21.3.20240124
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.
25 Jan 2024 membrain-seg updated to version 0.0.1
3D membrane segmentation for cryo-electron tomography.
25 Jan 2024 DFC updated to version 20240124
This application is intended to evaluate coevolutionary structural predictions of fold-switching proteins. State-of-the art algorithms predict that these fold-switching proteins assume only one stable structure. We hypothesize that coevolutionary signatures are being missed. Fold-switching proteins have the ability to transition between two sets of stable secondary and tertiary structure. The approach successfully revealed coevolution of amino acid pairs uniquely corresponding to both conformations of 56 fold-switching proteins from distinct families.
25 Jan 2024 CytoSPACE updated to version 1.0.6
CytoSPACE implements an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, it outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.
24 Jan 2024 nedit updated to version 5.7
NEdit is an GUI style editor for plain text and source code files. It provides mouse based editing and a streamlined editing style, based on popular Macintosh and MS Windows editors, using the X-window system. NEdit requires an X-based workstation or X-Terminal. Type nedit [filename] to edit a file.
24 Jan 2024 ESS updated to version 24.01.0
Emacs Speaks Statistics is an Emacs mode for interactive statistical programming and data analysis. Languages supported: the S family (S, S-PLUS and R), SAS, BUGS/JAGS, Stata and XLispStat. First load an R module per our R applications page. Putting the line (load "/usr/local/share/emacs/site-lisp/ess-17.11/lisp/ess-site") in your .emacs file, or its one-time equivalent M-x load-library /usr/local/share/emacs/site-lisp/ess-17.11/lisp/ess-site, will make an *ESS* buffer available.
23 Jan 2024 colabfold updated to version 1.5.5
ColabFold batch scripts
23 Jan 2024 napu updated to version R9
Napu (Nanopore Analysis Pipeline) is a collection of WDL workflows for variant calling and de novo assembly of ONT data,
23 Jan 2024 bakta updated to version 1.9.1
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
22 Jan 2024 ClinSV updated to version 1.1
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
19 Jan 2024 XAR updated to version 1.8.0.417.1
eXtensible ARchiver
19 Jan 2024 pomoxis updated to version 0.3.15
Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. Notably tools are included for generating and analysing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies.
18 Jan 2024 syri updated to version 1.6.3
Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
18 Jan 2024 ripgrep updated to version 13.0.0
ripgrep, a modern line-oriented search tool providing rg
17 Jan 2024 plotsr updated to version 1.1.0
Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.
17 Jan 2024 bonito updated to version 0.7.3
A PyTorch Basecaller for Oxford Nanopore Reads
17 Jan 2024 mirdeep2 updated to version 0.1.3
miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
17 Jan 2024 Hyperqueue updated to version 0.17.0
HyperQueue (HQ) lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups tasks into SLURM/PBS jobs and distributes them to fully utilize allocated nodes.
16 Jan 2024 sratoolkit updated to version 3.0.10
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
12 Jan 2024 R updated to version 4.3.2
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, ...).
12 Jan 2024 mbg updated to version 1.0.16
Minimizer based sparse de Bruijn Graph constructor.
12 Jan 2024 graphaligner updated to version 1.0.18
Seed-and-extend program for aligning long error-prone reads to genome graphs.
12 Jan 2024 victor updated to version 1.2beta
VICTOR (Variant Interpretation for Clinical Testing Or Research) is a pipeline that can be used for disease gene discovery research or clinical genetic testing
11 Jan 2024 samtools updated to version 1.19
The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library.
11 Jan 2024 pod5 updated to version 0.3.6
Tool for manipulating the pod5 format of nanopore reads
10 Jan 2024 dorado updated to version 0.5.1
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
10 Jan 2024 globus-cli updated to version 3.23.0
Globus command line interface
7 Jan 2024 rmblast updated to version 2.14.1
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.
7 Jan 2024 tandem-genotypes updated to version 1.9.1
tandem-genotypes finds changes in length of tandem repeats, from "long" DNA reads aligned to a genome.
5 Jan 2024 tetoolkit updated to version 2.2.3
A package for including transposable elements in differential enrichment analysis of sequencing datasets.
4 Jan 2024 peakachu updated to version 2.2.post1
A supervised learning framework for chromatin loop detection in genome-wide contact maps.
3 Jan 2024 curl updated to version 8.5.0
command line tool and library for transferring data with URLs
3 Jan 2024 scvitools updated to version 1.0.4
scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at UC Berkeley.
1 Jan 2024 antiSMASH updated to version 7.1.0
antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
31 Dec 2023 kallisto updated to version 0.50.1
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.
29 Dec 2023 nanopack updated to version 20231214
Tools for analyzing and processing long reads and alignments
28 Dec 2023 SciTE updated to version 5.4.1
SciTE or SCIntilla based Text Editor is a cross-platform text editor. Lightweight and built for speed, it is designed mainly for source editing, and performs syntax highlighting and inline function reference for many different languages.
27 Dec 2023 scomatic updated to version current
a tool that provides functionalities to detect somatic single-nucleotide mutations in high-throughput single-cell genomics and transcriptomics data sets, such as single-cell RNA-seq and single-cell ATAC-seq
19 Dec 2023 Trinotate updated to version 4.0.2
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
19 Dec 2023 neovim updated to version 0.9.5
Neovim is a refactor, and sometimes redactor, in the tradition of Vim (which itself derives from Stevie). It is not a rewrite but a continuation and extension of Vim.
16 Dec 2023 qsiprep updated to version 0.19.1
qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data.
11 Dec 2023 metaWRAP updated to version 1.3.2
MetaWRAP is a modular pipeline for shotgun metagenomic data analysis. It deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly.
10 Dec 2023 LAST updated to version 1519
LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
  • Finding rearrangements and recombinations (last-split)
  • Finding DNA-versus-protein related regions, especially protein fossils.
  • Unusual data, e.g. AT-rich DNA, because it can fit parameters to the data and calculate significance.
  • Sensitive DNA-DNA search, due to fitting, sensitive seeding, and calculating significance.
10 Dec 2023 smrtanalysis updated to version 13.0.0.207600
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.
10 Dec 2023 hifiasm updated to version 0.19.8
Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. Its latest release supports telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. It can produce better haplotype-resolved assemblies when given parental short reads or Hi-C data.
7 Dec 2023 salmon updated to version 1.10.1
a tool for quantifying the expression of transcripts using RNA-seq data.
6 Dec 2023 cellbender updated to version 0.3.1
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell omics data, including scRNA-seq, snRNA-seq, and CITE-seq.
Scientific Databases updated in last 3 months

For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data