Difference between revisions of "Bioinformatics Software"

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This is the list of software that is installed on the cluster.
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To use the software you need to use the '''module''' command with the name in the module column.
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module load <name_of_module>
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When you see '''None''' in module column it means the software is already in the path and no action needs to be taken.
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'''Container''' means that the software is embedded in a Singularity container. The singularity module should be loaded first to work with it.
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module load singularity
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Here is a wiki on working with containers: https://wiki.cs.huji.ac.il/wiki/Containers
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To see a list of all software that can be used by loading modules use this command
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module avail
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{| class="wikitable"
 
{| class="wikitable"
! Name !! Description
+
! Name !! Module !! Description
 
|-
 
|-
| Bamtools || BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files
+
| [http://annovar.openbioinformatics.org/en/latest/ Annovar] || None || ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)
 
|-
 
|-
| Bedops || BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
+
| [https://aws.amazon.com/cli/ aws cli] || None || AWS command line version 2
 
|-
 
|-
| Bedtools || A swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF
+
| [https://github.com/pezmaster31/bamtools Bamtools] || bio || BamTools provides both a programmer's API and an end user's toolkit for handling BAM files
 
|-
 
|-
| Biscuit || A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+
| [https://basemount.basespace.illumina.com/ Basemount] || none || BaseMount allows you to explore through runs, projects, samples, app results and analyses on Basespace and interact directly with the associated files exactly as you would with any other file system
 
|-
 
|-
| Bismark || 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
+
| [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html Bcl2fastq] || bcl2fastq/2.20.0 || bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis
 
|-
 
|-
| Boost & Boost-cpp || Boost provides free peer-reviewed portable C++ source libraries
+
| [https://github.com/samtools/bcftools BCFtools] || samtools/1.9 samtools/1.10 || a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
 
|-
 
|-
| Bsmap || 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
+
| [https://anaconda.org/bioconda/ucsc-bedgraphtobigwig bedgraphtobigwig] || bedgraphtobw/377 || Convert a bedGraph file to bigWig format
 
|-
 
|-
| Cellranger || Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis. Cell Ranger includes four pipelines relevant to single-cell gene expression experiments
+
| [https://bedops.readthedocs.io/en/latest/ Bedops] || bio || BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
 
|-
 
|-
| Circos || Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions
+
| [https://bedtools.readthedocs.io/en/latest/index.html Bedtools] || bio || A swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF
 
|-
 
|-
| Darts || Deep-learning Augmented RNA-seq analysis of Transcript Splicing
+
| [https://github.com/lh3/bioawk Bioawk] || none || Bioawk supports several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names
 
|-
 
|-
| Eigensoft || The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypesmaximizing power to detect true associations.
+
| [https://biopython.org/ BioPython] || biopython || Collection of freely available tools for computational molecular biology
 
|-
 
|-
| Emase || Expectation-Maximization algorithm for Allele Specific Expression
+
| [https://github.com/huishenlab/biscuit Biscuit] || bio || A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
 
|-
 
|-
| Finestruc || fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data
+
| [https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Bismark] || bismark || 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 analyze the methylation levels of their samples straight away
 
|-
 
|-
| Gatk || The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data
+
| [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs Blast] || blast || BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit
 
|-
 
|-
| Gatk4 || The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data
+
| [https://www.boost.org/ Boost & Boost-cpp] || bio || Boost provides free peer-reviewed portable C++ source libraries
 
|-
 
|-
| Gsl || The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
+
| [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2] || bowtie2 || An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
 
|-
 
|-
| Homer || Software for motif discovery and next generation sequencing analysis
+
| [https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview bs & bs-cp] || none || Command line interface for the BaseSpace Sequence Hub data
 
|-
 
|-
| Igblast || A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences
+
| [https://code.google.com/archive/p/bsmap/ Bsmap] || bio || BSMAP is a short reads mapping software for bisulfite sequencing reads
 
|-
 
|-
| Igv || Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
+
| [https://github.com/zyndagj/BSMAPz bsmapz] || bsmapz || An optimized fork of BSMAP. BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leaves 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
 
|-
 
|-
| Igvtools || command line tools for IGV
+
| [http://busco.ezlab.org/ Busco] || tib || BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB
 
|-
 
|-
| Macs2 || Model Based Analysis for ChIP-Seq data
+
| [https://github.com/cancerit/BRASS Brass] || container || Analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints
 
|-
 
|-
| Mafft || Multiple alignment program for amino acid or nucleotide sequences
+
| [http://jordan.biology.gatech.edu/page/software/broadpeak/index.html BroadPeak] || None || BroadPeak calling algorithm for diffuse ChIP-seq datasets
 
|-
 
|-
| Meme || Motif based sequence Analysis tools
+
| [https://github.com/lh3/bwa BWA] || elkind || The BWA read mapper
 
|-
 
|-
| Mirdeep2 || A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs
+
| [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger Cellranger] || cellranger || Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices, and perform clustering and gene expression analysis. Cell Ranger includes four pipelines relevant to single-cell gene expression experiments
 
|-
 
|-
| Peakachu || Peak calling tool for CLIP-seq data
+
| [http://www.rbvi.ucsf.edu/chimerax/ Chimerax] || chimerax || UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program
 
|-
 
|-
| Plink || Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
+
| [http://circos.ca/ Circos] || bio || Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions
 
|-
 
|-
| r-ichorcna || Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing
+
| [https://github.com/Teichlab/cellphonedb CellPhoneDB] || cellphonedb || CellPhoneDB is a publicly available repository of curated receptors, ligands, and its interactions
 
|-
 
|-
| Randfold ||  
+
| [https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index CRISPRCasFinder] || container || Enables the easy detection of CRISPRs and cas genes in user-submitted sequence data
 
|-
 
|-
| Rmats || MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data
+
| [https://github.com/NCIP/Trinity_CTAT/wiki CTAT] || container || The Trinity Cancer Transcriptome Analysis Toolkit (CTAT) aims to provide tools for leveraging RNA-Seq to gain insights into the biology of cancer transcriptomes
 
|-
 
|-
| Salmon || Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
+
| [https://cutadapt.readthedocs.io/en/stable/index.html Cutadapt] || cutadapt/1.18 (Python 2) cutadapt/2.10 (Python 3) || Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
 
|-
 
|-
| Tetoolkit || Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions
+
| [https://github.com/brentp/cyvcf2 cyvcf2] || cyvcf2 || A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files
 +
|-
 +
| [https://github.com/owenjm/damidseq_pipeline damidseq_pipeline] || damidseq || A single script that automatically handles sequence alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation
 
|-
 
|-
| Tobias || TOBIAS - Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
+
| [https://github.com/Xinglab/DARTS Darts] || darts || Deep-learning Augmented RNA-seq analysis of Transcript Splicing
 
|-
 
|-
| Viennarna || Vienna RNA package -- RNA secondary structure prediction and comparison
+
| [https://github.com/deeptools/deepTools Deeptools] || deeptools || A set of user-friendly tools for normalization and visualzation of deep-sequencing data
 
|-
 
|-
| Weblogo || Web based application designed to make the generation of sequence logos as easy and painless as possible
+
| [https://dropest.readthedocs.io/en/latest/index.html DropEst] || velocyto || Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements
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|-
 +
| [https://www.dnanexus.com/ Dxpy] || dxpy|| Command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform
 +
|-
 +
| [https://github.com/DReichLab/EIG Eigensoft] || eigensoft || The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes maximizing power to detect true associations.
 +
|-
 +
| [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastqc] || elkind || A quality control tool for high throughput sequence data
 +
|-
 +
| [https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure.html Finestruc] || bio || fine-structure is a fast and powerful algorithm for identifying population structure using dense sequencing data
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|-
 +
| [https://gatk.broadinstitute.org/hc/en-us Gatk] || bio || The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data
 +
|-
 +
| [https://gatk.broadinstitute.org/hc/en-us Gatk4] || gatk4 || The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data
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|-
 +
| [https://github.com/erhard-lab/gedi/wiki/GRAND-SLAM GRAND-SLAM] || slam || Globally refined analysis of newly transcribed RNA and decay rates using SLAM-seq
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|-
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| [https://www.gnu.org/software/gsl/ Gsl] || bio || The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
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|-
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| [http://www.bioinformatics.babraham.ac.uk/projects/hicup/ HiCUP] || hicup || A tool for mapping and performing quality control on Hi-C data
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|-
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| [http://homer.ucsd.edu/homer/index.html Homer] || homer || Software for motif discovery and next-generation sequencing analysis
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|-
 +
| [https://htseq.readthedocs.io/en/master/overview.html HTSeq] || htseq || A Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments
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|-
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| [https://ibamr.github.io/index IBAMR] || None || IBAMR is a distributed-memory parallel implementation of the immersed boundary (IB) method with support for Cartesian grid adaptive mesh refinement (AMR)
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|-
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| [https://github.com/kundajelab/idr IDR] || idr || 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
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|-
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| [http://www.ncbi.nlm.nih.gov/projects/igblast/ Igblast] || blast || A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences
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|-
 +
| [http://www.broadinstitute.org/software/igv/home Igv] || igv || Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
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|-
 +
| [http://www.broadinstitute.org/igv/ Igvtools] || igv || command-line tools for IGV
 +
|-
 +
| [https://www.ilastik.org/index.html Ilastik] || ilastik || Interactive learning and segmentation toolkit
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|-
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| [https://integrativemodeling.org/ IMP] || imp || IMP provides an open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. IMP can also be used from the Chimera molecular modeling system
 +
|-
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| [http://www.iqtree.org/ Iqtree] || tib || Efficient phylogenomic software by maximum likelihood
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|-
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| [http://mcmc-jags.sourceforge.net/ Jags & Rjags] || jags || JAGS is Just Another Gibbs Sampler. Rjags is an interface to the JAGS MCMC library
 +
|-
 +
| [https://davidaknowles.github.io/leafcutter/index.html LeafCutter] || r4 || Leafcutter quantifies RNA splicing variation using short-read RNA-seq data
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|-
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| [https://github.com/taoliu/MACS/ Macs2] || macs2 || Model-Based Analysis for ChIP-Seq data
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|-
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| [https://mafft.cbrc.jp/alignment/software/ Mafft] || bio || Multiple alignment program for amino acid or nucleotide sequences
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|-
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| [https://ncbi.github.io/magicblast/ Magicblast] || blast || NCBI BLAST next generation read mapper
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|-
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| [https://github.com/lh3/minimap2 Minimap2] || elkind || A versatile pairwise aligner for genomic and spliced nucleotide sequences
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|-
 +
| [http://mirexpress.mbc.nctu.edu.tw/index.php miRExpress] || None || Analyzing high-throughput sequencing data for profiling microRNA expression
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|-
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| [https://watson.hgen.pitt.edu/docs/mega2_html/mega2.html Mega2] || None || “Manipulation Environment for Genetic Analyses” A data-handling program for facilitating genetic linkage and association analyses
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|-
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| [https://github.com/daler/metaseq Metaseq] || metaseq || Integrative analysis of high-thoughput sequencing data
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|-
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| [http://smithlabresearch.org/software/methpipe/ Methpipe] || methpipe || A computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS)
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|-
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| [http://www.johnsonlab.ucsf.edu/mochi Mochiview] || mochiview || MochiView is Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis
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|-
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| [http://meme-suite.org/ Meme] || meme || Motif based sequence Analysis tools
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|-
 +
| [https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep Mirdeep2] || bio || A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs
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|-
 +
| [https://github.com/OpenGene/genefuse Mutscan] || mutscan || Detect and visualize target mutations by scanning FastQ files directly
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|-
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| [http://nucleoatac.readthedocs.io/en/latest/ NucleoATAC] || nucleoatac || Python package for calling nucleosomes using ATAC-Seq data. Also includes general scripts for working with paired-end ATAC-Seq data
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|-
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| [https://zhanglab.c2b2.columbia.edu/index.php/OLego OLego] || none || A program specifically designed for de novo spliced mapping of mRNA-seq reads
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|-
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| [https://github.com/tbischler/PEAKachu Peakachu] || peakachu || Peak calling tool for CLIP-seq data
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|-
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| [http://stephenslab.uchicago.edu/phase/download.html Phase] || None || Reconstructing haplotypes from population data
 +
|-
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| [http://compgen.cshl.edu/phast/ Phast] || phast || Phylogenetic Analysis with Space/Time models
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|-
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| [http://broadinstitute.github.io/picard/ Picard] || picard || Java tools for working with NGS data in the BAM format
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|-
 +
| [https://www.cog-genomics.org/plink/2.0/ Plink1.9 & Plink2] || None || Whole-genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
 +
|-
 +
| [https://github.com/EGA-archive/ega-download-client pyEGA3] || pyega3 || The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets
 +
|-
 +
| [https://pysam.readthedocs.io/en/latest/api.html Pysam] || samtools/1.9 samtools/1.10 || An interface for reading and writing SAM files
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|-
 +
| [https://qiime2.org/ Qiime2] || qiime || A next-generation microbiome bioinformatics platform
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|-
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| [http://qualimap.bioinfo.cipf.es/ Qualimap] || qualimap || Quality control of alignment sequencing data and its derivatives like feature counts
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|-
 +
| [https://www.r-project.org/ R ver 4] || r4 || R is a free software environment for statistical computing and graphics
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|-
 +
| [https://github.com/broadinstitute/ichorCNA r-ichorcna] || bio || Estimating tumor fraction in cell-free DNA from ultra-low-pass whole-genome sequencing
 +
|-
 +
| Randfold || bio || Minimum free energy of folding randomization test software
 +
|-
 +
| [https://rclone.org/ Rclone] || rclone || A command line program to manage files on cloud storage
 +
|-
 +
| [https://regtools.readthedocs.io/en/latest/ Regtools] || none || A set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context
 +
|-
 +
| [https://www3.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page Relion] || relion || RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)
 +
|-
 +
| [http://rnaseq-mats.sourceforge.net/ Rmats] || rmats || MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data
 +
|-
 +
| [https://github.com/Xinglab/rmats2sashimiplot rmats2sashimiplot] || rmats || A tool that generates sahimi plots from rMATS outputs
 +
|-
 +
| [https://deweylab.github.io/RSEM/ rsem] || rsem || RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data
 +
|-
 +
| [https://github.com/COMBINE-lab/salmon Salmon] || salmon || Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
 +
|-
 +
| [https://github.com/LiuzLab/SalmonTE SalmonTE] || salmonte || Ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data
 +
|-
 +
| [https://github.com/samtools/samtools SAMtools] || samtools/1.9 samtools/1.10 || Tools for dealing with SAM, BAM and CRAM files. Version 1.9 is for Python 2.7 and version 1.10 is for Python 3.7
 +
|-
 +
| [http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ Seqmonk] || seqmonk || Visualize and analyze high throughput mapped sequence data
 +
|-
 +
| [https://github.com/lh3/seqtk Seqtk] || elkind || A fast and lightweight tool for processing sequences in the FASTA or FASTQ format
 +
|-
 +
| [https://github.com/shenwei356/seqkit Seqkit] || elkind || Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
 +
|-
 +
| [http://t-neumann.github.io/slamdunk/index.html Slamdunk] || slam || SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis
 +
|-
 +
| [https://snakemake.readthedocs.io/en/stable/index.html Snakemake] || snakemake || The Snakemake workflow management system is a tool to create reproducible and scalable data analyses
 +
|-
 +
| [https://bioinfo.lifl.fr/sortmerna/sortmerna.php SortMeRNA] || none || A program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data
 +
|-
 +
| [https://cab.spbu.ru/software/spades/ Spades] || none || SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines
 +
|-
 +
| [https://www.statsmodels.org/stable/index.html Statsmodel] || bio || A Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration
 +
|-
 +
| [https://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism/README SRprism] || blast || Single Read Paired Read Indel Substitution Minimizer
 +
|-
 +
| [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc Sratoolkit] || sratoolkit || A set of compiled binaries and corresponding source code for tools that download, manipulate and validate next-generation sequencing data stored in the NCBI SRA archive
 +
|-
 +
| [https://github.com/alexdobin/STAR STAR] || None || Spliced Transcripts Alignment to a Reference
 +
|-
 +
| [https://github.com/STAR-Fusion/STAR-Fusion/wiki STAR-Fusion] || container || STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads
 +
|-
 +
| [http://subread.sourceforge.net/ Subread] || bio || The Subread package comprises a suite of software programs for processing next-gen sequencing read data
 +
|-
 +
| [https://github.com/walaj/svaba SvABA] || svaba || A method for detecting structural variants in sequencing data using genome-wide local assembly
 +
|-
 +
| [http://hammelllab.labsites.cshl.edu/software#TEToolkit Tetoolkit] || tetoolkit || Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions
 +
|-
 +
| [http://hammelllab.labsites.cshl.edu/software/#TEtranscripts TEtranscripts] || tetranscripts || A package for including transposable elements in differential enrichment analysis of sequencing datasets
 +
|-
 +
| [https://github.com/loosolab/TOBIAS/ Tobias] || tobias || TOBIAS - Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
 +
|-
 +
| [https://github.com/CGATOxford/UMI-tools UMI-tools] || umitools || Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
 +
|-
 +
| [https://github.molgen.mpg.de/loosolab/UROPA Uropa] || tobias || UROPA (Universal RObust Peak Annotator) is a command-line based tool, intended for genomic region annotation from e.g. peak calling. It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction, and strand into account. Furthermore, it allows filtering for GTF attribute values, e.g. protein_coding
 +
|-
 +
| [https://ccb.jhu.edu/software/tophat/index.shtml TopHat] || tophat || 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
 +
|-
 +
| [https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ trim_galore] || trim_galore/0.3.7 trim_galore/0.6.5 || Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality
 +
|-
 +
| [http://www.usadellab.org/cms/?page=trimmomatic Trimmomatic] || elkind || A flexible read trimming tool for Illumina NGS data
 +
|-
 +
| [https://github.com/trinityrnaseq/trinityrnaseq/ Trinity] || tib || Trinity assembles transcript sequences from Illumina RNA-Seq data
 +
|-
 +
| [https://vcftools.github.io/ Vcftools] || bio || A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries
 +
|-
 +
| [http://www.tbi.univie.ac.at/RNA/ Viennarna] || bio || Vienna RNA package -- RNA secondary structure prediction and comparison
 +
|-
 +
| [http://velocyto.org/velocyto.py/index.html Velocyto] || velocyto || A library for the analysis of RNA velocity
 +
|-
 +
| [http://www.ensembl.org/info/docs/tools/vep/index.html VEP] || vep || VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Cached data is in /usr/local/bioinfo/vep-data
 +
|-
 +
| [http://weblogo.berkeley.edu/ Weblogo] || bio || Web-based application designed to make the generation of sequence logos as easy and painless as possible
 
|}
 
|}
 
  
 
[[Category:Bio Informatics]]
 
[[Category:Bio Informatics]]
'''Software installed in Bioinformatics cluster'''
 
 
= PEAKachu =
 
Peak calling tool for CLIP-seq data
 
 
[https://github.com/tbischler/PEAKachu Github]
 
 
To use run this command
 
 
module load peakachu
 
 
= FastUniq =
 
An ultrafast de novo tool for removal of duplicates in paired short DNA sequence reads in FASTQ format
 
 
[https://sourceforge.net/projects/fastuniq/files/ SourceForge]
 
 
= cmpfastq =
 
A simple Perl program that allows the user to compare QC filtered fastq files
 
 
[http://compbio.brc.iop.kcl.ac.uk/software/cmpfastq.php Home page]
 
 
 
= STAR =
 
Ultrafast universal RNA-seq aligner
 
 
[https://github.com/alexdobin/STAR Github]
 
 
Installed version: 2.7.3a
 
 
 
= Bedtools =
 
Bedtools is a fast, flexible toolset for genome arithmetic.
 
 
[https://bedtools.readthedocs.io/en/latest/ Webpage]
 
 
Installed version: 2.29.0
 
 
Usage:
 
 
module load bedtools
 
 
= GATK =
 
Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.
 
 
The tools can be used individually or chained together into complete workflows.
 
 
[https://software.broadinstitute.org/gatk/documentation/ Webpage]
 
 
Installed version: 4.1.3.0
 
 
Usage:
 
 
module load gatk
 
 
= SourceTracker2 =
 
SourceTracker is a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments.
 
 
[https://github.com/biota/sourcetracker2 Webpage]
 
 
Usage:
 
 
module load conda-st2
 

Latest revision as of 17:44, 18 April 2021

This is the list of software that is installed on the cluster.

To use the software you need to use the module command with the name in the module column.

module load <name_of_module>

When you see None in module column it means the software is already in the path and no action needs to be taken.

Container means that the software is embedded in a Singularity container. The singularity module should be loaded first to work with it.

module load singularity

Here is a wiki on working with containers: https://wiki.cs.huji.ac.il/wiki/Containers

To see a list of all software that can be used by loading modules use this command

module avail
Name Module Description
Annovar None ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)
aws cli None AWS command line version 2
Bamtools bio BamTools provides both a programmer's API and an end user's toolkit for handling BAM files
Basemount none BaseMount allows you to explore through runs, projects, samples, app results and analyses on Basespace and interact directly with the associated files exactly as you would with any other file system
Bcl2fastq bcl2fastq/2.20.0 bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis
BCFtools samtools/1.9 samtools/1.10 a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
bedgraphtobigwig bedgraphtobw/377 Convert a bedGraph file to bigWig format
Bedops bio BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
Bedtools bio A swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF
Bioawk none Bioawk supports several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names
BioPython biopython Collection of freely available tools for computational molecular biology
Biscuit bio A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Bismark bismark 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 analyze the methylation levels of their samples straight away
Blast blast BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit
Boost & Boost-cpp bio Boost provides free peer-reviewed portable C++ source libraries
Bowtie2 bowtie2 An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
bs & bs-cp none Command line interface for the BaseSpace Sequence Hub data
Bsmap bio BSMAP is a short reads mapping software for bisulfite sequencing reads
bsmapz bsmapz An optimized fork of BSMAP. BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leaves 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 tib BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB
Brass container Analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints
BroadPeak None BroadPeak calling algorithm for diffuse ChIP-seq datasets
BWA elkind The BWA read mapper
Cellranger cellranger Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices, and perform clustering and gene expression analysis. Cell Ranger includes four pipelines relevant to single-cell gene expression experiments
Chimerax chimerax UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program
Circos bio Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions
CellPhoneDB cellphonedb CellPhoneDB is a publicly available repository of curated receptors, ligands, and its interactions
CRISPRCasFinder container Enables the easy detection of CRISPRs and cas genes in user-submitted sequence data
CTAT container The Trinity Cancer Transcriptome Analysis Toolkit (CTAT) aims to provide tools for leveraging RNA-Seq to gain insights into the biology of cancer transcriptomes
Cutadapt cutadapt/1.18 (Python 2) cutadapt/2.10 (Python 3) Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
cyvcf2 cyvcf2 A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files
damidseq_pipeline damidseq A single script that automatically handles sequence alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation
Darts darts Deep-learning Augmented RNA-seq analysis of Transcript Splicing
Deeptools deeptools A set of user-friendly tools for normalization and visualzation of deep-sequencing data
DropEst velocyto Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements
Dxpy dxpy Command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform
Eigensoft eigensoft The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes maximizing power to detect true associations.
Fastqc elkind A quality control tool for high throughput sequence data
Finestruc bio fine-structure is a fast and powerful algorithm for identifying population structure using dense sequencing data
Gatk bio The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data
Gatk4 gatk4 The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data
GRAND-SLAM slam Globally refined analysis of newly transcribed RNA and decay rates using SLAM-seq
Gsl bio The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
HiCUP hicup A tool for mapping and performing quality control on Hi-C data
Homer homer Software for motif discovery and next-generation sequencing analysis
HTSeq htseq A Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments
IBAMR None IBAMR is a distributed-memory parallel implementation of the immersed boundary (IB) method with support for Cartesian grid adaptive mesh refinement (AMR)
IDR idr 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
Igblast blast A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences
Igv igv Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
Igvtools igv command-line tools for IGV
Ilastik ilastik Interactive learning and segmentation toolkit
IMP imp IMP provides an open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. IMP can also be used from the Chimera molecular modeling system
Iqtree tib Efficient phylogenomic software by maximum likelihood
Jags & Rjags jags JAGS is Just Another Gibbs Sampler. Rjags is an interface to the JAGS MCMC library
LeafCutter r4 Leafcutter quantifies RNA splicing variation using short-read RNA-seq data
Macs2 macs2 Model-Based Analysis for ChIP-Seq data
Mafft bio Multiple alignment program for amino acid or nucleotide sequences
Magicblast blast NCBI BLAST next generation read mapper
Minimap2 elkind A versatile pairwise aligner for genomic and spliced nucleotide sequences
miRExpress None Analyzing high-throughput sequencing data for profiling microRNA expression
Mega2 None “Manipulation Environment for Genetic Analyses” A data-handling program for facilitating genetic linkage and association analyses
Metaseq metaseq Integrative analysis of high-thoughput sequencing data
Methpipe methpipe A computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS)
Mochiview mochiview MochiView is Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis
Meme meme Motif based sequence Analysis tools
Mirdeep2 bio A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs
Mutscan mutscan Detect and visualize target mutations by scanning FastQ files directly
NucleoATAC nucleoatac Python package for calling nucleosomes using ATAC-Seq data. Also includes general scripts for working with paired-end ATAC-Seq data
OLego none A program specifically designed for de novo spliced mapping of mRNA-seq reads
Peakachu peakachu Peak calling tool for CLIP-seq data
Phase None Reconstructing haplotypes from population data
Phast phast Phylogenetic Analysis with Space/Time models
Picard picard Java tools for working with NGS data in the BAM format
Plink1.9 & Plink2 None Whole-genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
pyEGA3 pyega3 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets
Pysam samtools/1.9 samtools/1.10 An interface for reading and writing SAM files
Qiime2 qiime A next-generation microbiome bioinformatics platform
Qualimap qualimap Quality control of alignment sequencing data and its derivatives like feature counts
R ver 4 r4 R is a free software environment for statistical computing and graphics
r-ichorcna bio Estimating tumor fraction in cell-free DNA from ultra-low-pass whole-genome sequencing
Randfold bio Minimum free energy of folding randomization test software
Rclone rclone A command line program to manage files on cloud storage
Regtools none A set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context
Relion relion RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)
Rmats rmats MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data
rmats2sashimiplot rmats A tool that generates sahimi plots from rMATS outputs
rsem rsem RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data
Salmon salmon Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
SalmonTE salmonte Ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data
SAMtools samtools/1.9 samtools/1.10 Tools for dealing with SAM, BAM and CRAM files. Version 1.9 is for Python 2.7 and version 1.10 is for Python 3.7
Seqmonk seqmonk Visualize and analyze high throughput mapped sequence data
Seqtk elkind A fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Seqkit elkind Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Slamdunk slam SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis
Snakemake snakemake The Snakemake workflow management system is a tool to create reproducible and scalable data analyses
SortMeRNA none A program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data
Spades none SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines
Statsmodel bio A Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration
SRprism blast Single Read Paired Read Indel Substitution Minimizer
Sratoolkit sratoolkit A set of compiled binaries and corresponding source code for tools that download, manipulate and validate next-generation sequencing data stored in the NCBI SRA archive
STAR None Spliced Transcripts Alignment to a Reference
STAR-Fusion container STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads
Subread bio The Subread package comprises a suite of software programs for processing next-gen sequencing read data
SvABA svaba A method for detecting structural variants in sequencing data using genome-wide local assembly
Tetoolkit tetoolkit Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions
TEtranscripts tetranscripts A package for including transposable elements in differential enrichment analysis of sequencing datasets
Tobias tobias TOBIAS - Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
UMI-tools umitools Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
Uropa tobias UROPA (Universal RObust Peak Annotator) is a command-line based tool, intended for genomic region annotation from e.g. peak calling. It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction, and strand into account. Furthermore, it allows filtering for GTF attribute values, e.g. protein_coding
TopHat tophat 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
trim_galore trim_galore/0.3.7 trim_galore/0.6.5 Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality
Trimmomatic elkind A flexible read trimming tool for Illumina NGS data
Trinity tib Trinity assembles transcript sequences from Illumina RNA-Seq data
Vcftools bio A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries
Viennarna bio Vienna RNA package -- RNA secondary structure prediction and comparison
Velocyto velocyto A library for the analysis of RNA velocity
VEP vep VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Cached data is in /usr/local/bioinfo/vep-data
Weblogo bio Web-based application designed to make the generation of sequence logos as easy and painless as possible