Applications and Scientific Database Updates

Application updates in the last 3 months

To see all versions available for any application, use module avail application_name
All centrally-installed applications are listed on the Applications page

Updated	Application
5 Jul 2022	jemalloc updated to version 5.3.0 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
5 Jul 2022	autoconf updated to version 2.71 Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.
1 Jul 2022	sambamba updated to version 0.8.2 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.
29 Jun 2022	DNAnexus updated to version 0.326.0 DNAnexus is a cloud-based commercial solution for next-generation sequence analysis and visualization. It has a command-line interface (CLI) which can be used to log in to the DNAnexus platform, upload and navigate data, and launch analyses.
29 Jun 2022	TElocal updated to version 1.1.2 TElocal: a tool that utilizes both uniquely and ambiguously mapped reads to quantify transposable element expression at the locus level.
28 Jun 2022	scChromHMM updated to version 20220610 scChromHMM provides a suite of tools for rapid processing of single-cell histone modification data to perform chromatin states analysis of the genome within each single-cell. It is an extention of bulk ChromHMM framework, which consumes the HMM model learned from ChromHMM and perform chromatin state analysis by running forward-backward algorithm for each single-cell.
27 Jun 2022	Neuron updated to version 7.7 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.
27 Jun 2022	XHMM updated to version 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.
27 Jun 2022	samblaster updated to version 0.1.26 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.
27 Jun 2022	nanopolish updated to version 0.14.0 nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).
24 Jun 2022	MIPAV updated to version 11.0.3 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.
24 Jun 2022	fragpipe updated to version 18.0 FragPipe is a Java Graphical User Interface (GUI) and CLI workflow tool for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger.
24 Jun 2022	ea-utils updated to version 1.04.807 Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc.
24 Jun 2022	MUSCLE updated to version 5.1 Fast Multiple Sequence Alignment program.
23 Jun 2022	STAR updated to version 2.7.9a Spliced Transcripts Alignment to a Reference
23 Jun 2022	ionquant updated to version 1.8.0 IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe (recommended option), but can also be run as a command-line tool.
23 Jun 2022	tmux updated to version 3.3a tmux is a terminal multiplexer. Type 'module load tmux' to load the module, then 'tmux --help'
23 Jun 2022	trimmomatic updated to version 0.39 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.
23 Jun 2022	philosopher updated to version 4.2.2 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.
23 Jun 2022	arcashla updated to version 0.5.0 high resolution HLA typing from RNA seq
23 Jun 2022	Genome Browser updated to version 432 The Genome Browser Mirror Fragments 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.
23 Jun 2022	Gromacs updated to version 2021.3 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.
23 Jun 2022	MuSE updated to version 2.0 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.
22 Jun 2022	xcp_d updated to version 0.0.9 xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies).
22 Jun 2022	pb-cpg-tools updated to version 1.1.0 Tools for analyzing CpG/5mC data from PacBio HiFi reads aligned to a reference genome
22 Jun 2022	shasta updated to version 0.10.0 De novo assembly from Oxford Nanopore reads
22 Jun 2022	Java updated to version 17.0.3.1 Java is a high-level language and software-only platform. The two main components of the Java platform are the Java Application Programming Interface (API), which is a library of Java command lines and the Java Virtual Machine (JVM) that interprets Java code into machine language.
22 Jun 2022	parallel updated to version 20220622 GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
22 Jun 2022	snpEff updated to version 5.1d snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).
21 Jun 2022	hisat updated to version 2.2.2.1-ngs3.0.0 HISAT is a fast and sensitive spliced alignment program which uses Hierarchical Indexing for Spliced Alignment of Transcripts.
21 Jun 2022	Beagle updated to version 5.4_18Mar22 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.
17 Jun 2022	Julia updated to version 1.7.3 high level, dynamic language for technical computing
17 Jun 2022	cpdf updated to version 2.5.1 Coherent PDF tools
17 Jun 2022	minimac updated to version 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.
16 Jun 2022	samtools updated to version 1.15.1 The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library.
16 Jun 2022	Emacs updated to version 28.1 Emacs is a text and source code editor for text terminals and X. It has a vast set of features and is well suited for doing everything from reading mail and simple text editing to managing and editing large programming projects. It has its own help and tutorial which can be accessed by typing Ctrl-h i and Ctrl-h t respectively. Type emacs [filename] to edit a file. For more info, see here.
16 Jun 2022	globus-cli updated to version 3.6.0 Globus command line interface
16 Jun 2022	NAMD updated to version 2.14 NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. VMD, the associated molecular visualization program, is also available.
16 Jun 2022	git updated to version 2.36.1 Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
16 Jun 2022	pandoc updated to version 2.18 Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.
15 Jun 2022	netcdf updated to version 4.9.0 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
15 Jun 2022	Grace updated to version 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.
15 Jun 2022	FFmpeg updated to version 5.0.1 A complete, cross-platform solution to record, convert and stream audio and video.
14 Jun 2022	sodium updated to version 1.0.18 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing, and more.
14 Jun 2022	Rstudio updated to version 2022.02.3-492 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.
14 Jun 2022	jags updated to version 4.3.1 Just another Gibbs sampler
14 Jun 2022	AutodockVina updated to version 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.
14 Jun 2022	Autodock updated to version 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.
14 Jun 2022	metal updated to version 2020-05-05 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.
14 Jun 2022	udunits updated to version 2.2.28 The UDUNITS-2 package provides support for units of physical quantities. Its three main components are: 1) (udunits2lib)a C library for units of physical quantities; 2) (udunits2prog)a utility; for obtaining the definition of a unit and for converting numeric values between compatible units; and 3) an extensive database of units.
14 Jun 2022	treetime updated to version 0.9.0 TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.
13 Jun 2022	Autodock-GPU updated to version 1.5.3 Autodock-GPU performs docking calculations, and processes ligand-receptor poses in parallel over multiple compute units on GPUs.
13 Jun 2022	asciinema updated to version 2.2.0 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.
10 Jun 2022	picard updated to version 2.27.3 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.
10 Jun 2022	mixcr updated to version 4.0.0 MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.
10 Jun 2022	gdal updated to version 3.5.0 GDAL is a translator library for raster and vector geospatial data formats
10 Jun 2022	SAIGE updated to version 1.0.9 R package for large-scale genetic association studies.
10 Jun 2022	proj updated to version 6.3.2 PROJ is a generic coordinate transformation software that transforms geospatial coordinates from one coordinate reference system (CRS) to another
9 Jun 2022	SQLite updated to version 3.38.5 SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.
9 Jun 2022	inkscape updated to version 1.2 Inkscape is a Free and open source vector graphics editor
9 Jun 2022	caper updated to version 2.1.3 A Python-based wrapper for the Cromwell pipeline system used by ENCODE pipelines. Includes the croo and qc2tsv commands for parsing Cromwell and quality control output.
8 Jun 2022	geos updated to version 3.10.3 GEOS is a C/C++ library for computational geometry with a focus on algorithms used in geographic information systems (GIS) software.
8 Jun 2022	nibabies updated to version 22.0.2 Preprocessing pipeline for neonate and infant MRI.
8 Jun 2022	R updated to version 4.2.0 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, ...).
7 Jun 2022	Gemini updated to version 0.30.2 GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very powerful system for exploring genetic variation for for disease and population genetics.
7 Jun 2022	phaser updated to version 1.1.1 phasing and Allele Specific Expression from RNA-seq. Performs haplotype phasing using read alignments in BAM format from both DNA and RNA based assays, and provides measures of haplotypic expression for RNA based assays.
7 Jun 2022	biom-format updated to version 2.1.12 tool (and library) to manipulate Biological Observation Matrix (BIOM) Format files
6 Jun 2022	chipseq_pipeline updated to version 2.1.6 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)
6 Jun 2022	deepvariant updated to version 1.4.0 DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
6 Jun 2022	clustalo updated to version 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.
6 Jun 2022	AnnotSV updated to version 3.1.1 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.
6 Jun 2022	CD-HIT updated to version 4.6.8 CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
4 Jun 2022	foldseek updated to version 1-2dd3b2f Fast structural similarity search
3 Jun 2022	seqkit updated to version 2.2.0 A cross-platform toolkit for FASTA/Q file manipulation
3 Jun 2022	csvkit updated to version 1.0.7 csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.
3 Jun 2022	FastTree updated to version 2.1.11 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.
3 Jun 2022	AfterQC updated to version 0.9.7 Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.
3 Jun 2022	admixture updated to version 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.
3 Jun 2022	ANTs updated to version 2.3.5 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.
1 Jun 2022	htseq updated to version 2.0.1 HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
1 Jun 2022	HMMER updated to version 3.3.2 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.
1 Jun 2022	MONAILabel updated to version 0.3.2; 0.4.0rc4 MONAI Label is a free and open-source platform that facilitates the development of AI-based applications that aim at reducing the time required to annotate 3D medical image datasets. It allows researchers to readily deploy their apps as services, which can be made available to clinicians via their preferred user-interface. Currently, MONAI Label readily supports locally installed (3DSlicer) and web-based (OHIF) frontends, and offers two Active learning strategies to facilitate and speed up the training of segmentation algorithms. MONAI Label allows researchers to make incremental improvements to their labeling apps by making them available to other researchers and clinicians alike.
31 May 2022	sratoolkit updated to version 3.0.0 The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
31 May 2022	GCTA updated to version 1.94.0beta0 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.
31 May 2022	bbtools updated to version 38.96 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.
31 May 2022	fastq_screen updated to version 0.15.2 FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
31 May 2022	Huygens updated to version 22.04.0-p0 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.
30 May 2022	deepab updated to version 1.2 DeepAb is antibody structure prediction using interpretable deep learning.
29 May 2022	MotionCor2 updated to version 1.4.5 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.
29 May 2022	PEGASAS updated to version 1.1.0 PEGASAS is a a computational framework for pathway enrichment-guided activity study of alternative splicing. It correlates transcriptional signatures of 50 different cancer driver pathways with alternative splicing events.
27 May 2022	macs updated to version 3 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.
27 May 2022	texinfo updated to version 6.8 Texinfo is the official documentation format of the GNU project
27 May 2022	Tex updated to version 2022 Tex + Latex + associated packages for high-quality text formatting.
27 May 2022	GD updated to version 2.3.3 GD is an open source code library for the dynamic creation of images by programmers.
26 May 2022	Hail updated to version 0.2.95 Hail is an open-source, scalable framework for exploring and analyzing genomic data.
26 May 2022	ImageMagick updated to version 7.1.0 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.
26 May 2022	crispresso updated to version 2.2.8 Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
25 May 2022	qsiprep updated to version 0.15.4 qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data.
24 May 2022	crossmap updated to version 0.6.3 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
24 May 2022	cellranger updated to version 7.0.0 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.
24 May 2022	novocraft updated to version 4.03.05 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.
24 May 2022	GSL updated to version 2.7 The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
24 May 2022	dmriprep updated to version 0.5.0 Pipeline for preprocessing diffusion MRI datasets.
23 May 2022	LJA updated to version 0.1 The La Jolla Assembler (LJA) is a tool for assemblies of long and accurate reads. It reduces the error rate in these reads by three orders of magnitude (making them nearly error-free) and constructs the de Bruijn graph for large genomes and large k-mer sizes. Since the de Bruijn graph constructed for a fixed k-mer size is typically either too tangled or too fragmented, LJA uses a new concept of a multiplex de Bruijn graph with varying k-mer sizes.
23 May 2022	Flexbar updated to version 3.5.0 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
23 May 2022	EDirect updated to version 17.1 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.
22 May 2022	nodejs updated to version 16.15.0 Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs
20 May 2022	stringtie updated to version 2.2.1 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.
20 May 2022	cryolo updated to version 1.8.3 Automated particle picker for cryo-EM
20 May 2022	snakemake updated to version 7.7.0 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.
20 May 2022	nextflow updated to version 22.04.0 Data-driven computational pipelines
19 May 2022	pvactools updated to version 3.0.1 pVACtools is a cancer immunotherapy suite consisting of pVACseq, pVACfuse, pVACvector
19 May 2022	manta updated to version 1.6.0-fork-jykr Structural variant and indel caller for mapped sequencing data
18 May 2022	biobambam2 updated to version 2.0.183-release-20210802180148 Tools for early stage alignment file processing.
18 May 2022	spark updated to version 3.2.1 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.
18 May 2022	Scala updated to version 3.1.2 General purpose language; multiparadigm (object-oriented, functional, concurrent elements); statically typed, type-safe
12 May 2022	smriprep updated to version 0.8.3 Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools).
12 May 2022	QIIME updated to version 2022.2 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).
11 May 2022	apptainer updated to version 1.0.2 Apptainer allows you to build and run Linux containers with emphasis on use in HPC. Apptainer is the Linux Foundation variant of and successor to the widely popular Singularity.
9 May 2022	MVAPICH2 updated to version 2.3.7 MPI implementation for Infiniband
6 May 2022	gmap-gsnap updated to version 2021-12-17 A Genomic Mapping and Alignment Programs
5 May 2022	hic_breakfinder updated to version 1.0 A framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines.
4 May 2022	patchelf updated to version 0.14 patchelf is a small utility to modify the dynamic linker and RPATH of ELF executables.
3 May 2022	mriqc updated to version 22.0.0 MRIQC is an MRI quality control tool
2 May 2022	trinity updated to version 2.14.0 Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
2 May 2022	guppy updated to version 6.1.2 Local accelerated basecalling for Nanopore data
28 Apr 2022	biobakery_workflows updated to version 3.0.0-alpha.7 bioBakery is a meta’omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of preconfigured analysis modules also joined into workflows for reproducibility. Each individual module has been developed to perform a particular task, e.g. quantitative taxonomic profiling or statistical analysis.
27 Apr 2022	Comsol updated to version 6.0.0.405 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.
27 Apr 2022	xpdf updated to version 4.04 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.
27 Apr 2022	netpbm updated to version 10.86.33 Netpbm is a toolkit for manipulation of graphic images, including conversion of images between a variety of different formats. There are over 300 separate tools in the package including converters for about 100 graphics formats. Examples of the sort of image manipulation we're talking about are: Shrinking an image by 10%; Cutting the top half off of an image; Making a mirror image; Creating a sequence of images that fade from one image to another.
26 Apr 2022	Mathematica updated to version 13.0.1 Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language.
26 Apr 2022	GATK updated to version 4.2.6.1 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.
25 Apr 2022	golang updated to version 1.18.1 The Go programming language
25 Apr 2022	tepeaks updated to version 0.1 TEpeaks takes ChIP-seq (and similar data) alignment files and identifies narrow ChIP peaks. It is an extension of MACS by adding the functionality of handling reads with multiple alignments. It also allows normalization by bin correlation.
25 Apr 2022	signalp updated to version 6.0g SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
25 Apr 2022	IGV updated to version 2.12.3 The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
25 Apr 2022	IGVTools updated to version 2.12.3 IGVTools provides utilities for working with ascii file formats used by the Integrated Genome Viewer. The files can be sorted, tiled, indexed, and counted.
25 Apr 2022	VEP updated to version 106 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.
25 Apr 2022	smrtanalysis updated to version 11.0 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.
22 Apr 2022	alphafold2 updated to version 2.2.0 This package provides an implementation of the protein structure inference pipeline of AlphaFold v2.0.
21 Apr 2022	neovim updated to version 0.7.0 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.
20 Apr 2022	ultraplex updated to version 1.2.5 Ultraplex is primarily designed for the demultiplexing of sequencing data generated using in-house library preparation protocols with custom adaptors
20 Apr 2022	SURVIVOR updated to version 1.0.7 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.
20 Apr 2022	delly updated to version 0.9.1 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.
19 Apr 2022	cutadapt updated to version 4.0 cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.
19 Apr 2022	rilseq updated to version 0.82 RILseq computational protocol
17 Apr 2022	nvchecker updated to version 2.8 nvchecker (short for new version checker) is for checking if a new version of some software has been released.
15 Apr 2022	iqmol updated to version 2.14.0 free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).
14 Apr 2022	anvio updated to version 7.1 Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics. It brings together many aspects of today’s cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.
14 Apr 2022	fastp updated to version 0.23.2 A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
14 Apr 2022	maxquant updated to version 2.1.0.0 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.
12 Apr 2022	Acemd updated to version 3.5.0 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.
12 Apr 2022	arriba updated to version 2.2.1 Arriba identifies gene fusions in RNA-Seq data. It also can detect other structural variants in genomic data, such as intron duplications and gene truncations.