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Software Catalog

The following bioinformatics applications are offered on a limited-support basis through the HPCC:

Application

Version

Description

Module File

A5

20130326 (default)

A genome assembly pipeline for bacteria and archaea that automates as much data cleaning and parameter selection as possible.

A5

Abyss

1.5.1, 1.3.6 (default), 1.3.5, 1.3.4, 1.3.3, 1.3.2, 1.2.5

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

ABySS

AlignACE

2004 (default)

A motif-finding algorithm

AlignACE

ALLPATHS-LG

41313

A short-read whole genome assembler

ALLPATHS

AmpliconNoise

1.25

A collection of programs for the removal of noise from 454 sequenced PCR amplicons

AmpliconNoise

Amos

3.1.0

A Modular, Open-Source whole genome assembler

AMOS

Analysis

0.8.1

A software packages for evolutionary genetic analysis

analysis

ANNOVAR

20140409 (default), 20130514, 20130417

Performs functional annotation of diverse genomes.

annovar

ARB

8210

A graphically oriented package comprising various tools for sequence database handling and data analysis

ARB

Augustus

2.7.0 (default), 2.5.5

Predicts genes in eukaryotic genomic sequences.

MAKER, augustus

autoadapt0.2 (default)Wrapper to fastqc and cutadapt that auto-detects and trims adapters from fastq-formatted readsautoadapt
bamaddrg20140611 (default)bamaddrg: adds read groups to input BAM files, streams BAM output on stdout.bamaddrg

BamBam

20130708 (default), 20130423, 20130422

A toolset for working with BAM files

BamBam

Bambus

2.0

General purpose scaffolding assembler - part of AMOS package

AMOS

BAMTools

2.2.3 (default), 1.0.2

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

BAMTools

BCFTools0.0.1 (default)Utilities for variant calling and manipulating VCFs and BCFs. Includes functionality of HTSlibbcftools
BEAGLE4.0 (default)

Performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

BEAGLE
BeagleLib

20130522 (default)

A general purpose library for evaluating the likelihood of sequence evolution of trees. Used by MrBayes

BeagleLib
BEDOPS2.4.5 (default)

Toolkit that performs boolean and other setup ops, statistics, archiving, and conversion of genomic data.

BEDOPS

BEDTools

2.17.0 (default), 2.12.0

Utilities used for common genomics tasks such as finding feature overlaps and computing coverage.

BEDTools

BELT

1.0.0 (default)

A peak caller.

BELT

BER

20051118

BLAST-Extend-Repraze (BER) is a package for identifying potential frameshifts or point mutations in a given open reading frame (ORF).

BER

Bioconductor

2.12

High throughput sequencing analysis tools in R. The newest version of R (non-default) contains the most comprehensive list of Bioconductor modules.  The system default version of R contains most, but not all of these modules (e.g. excludes xcms, CAMERA, vegan, some others)

R/3.0.1

Biomformat1.2.0 (default), 0.93Support applications for the biom general-use format for representing biological sample by observation contingency tablesbiomformat

Bioperl

1.6.923 (default), 1.6.901, 1.6.1

A collection of Perl modules for bioinformatics processing and analysis.

Bioperl

Biorithm

1.1 (default)

Biorithm is a C++ package that includes several libraries and software tools to analyze data in molecular systems biology.

Biorithm

BLAST

2.2.26 (default), 2.2.25, 2.2.23

Basic Local Alignment Search Tool

BLAST

BLAST+

2.2.30 (default), 2.2.29, 2.2.28 (default), 2.2.27, 2.2.25

Basic Local Alignment Search Tool (multi-threaded support)

BLAST+

Blast2go

2.5 (default)

Functional annotation of sequences and analysis of annotation data

blast2go

BLAT

34

BLAST-like alignment tool

BLAT

Bowtie

1.0.0 (default), 0.12.8, 0.12.7, 0.12.3

Ultrafast, memory-efficient short read DNA sequence aligner

bowtie

Bowtie22.2.3 (default), 2.2.1, 2.2.0, 2.1.0An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters.bowtie2
BreakDancer1.1.2 (default)BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.BreakDancer

BWA /
BWA-MEM

0.7.7.r441 (default), 0.7.5a.r428, 0.7.5a,r405, 0.5.9

BWA aligns relatively short nucleotide sequences against a long reference sequence.

bwa

CAP33.0 (default)An assemblerCAP3

CD-HIT

4.5.5

A very widely used program for clustering and comparing large sets of protein or nucleotide sequences.

CDHIT

CEGMA

2.4 (default), 2.3

Core Eukaryotic Genes Mapping Approach

CEGMA

Celera WGS

7.0 (default), 6.1

A de novo whole-genome shotgun (WGS) DNA sequence assembler.

wgscelera

Censor

4.2

Compares and masks protein or nucleotide sequences.

censor

Circonspect0.2.6 (default)

Circonspect is a bioinformatic tool to produce contig spectra, useful for the estimating viral diversity in metagenomes.

circonspect

CIRCOS

0.55

Displays data in a circular format.

CIRCOS

ClustalO

1.1.0

Multiple sequence alignment application based on ClustalW but with improved scalability.

ClustalO

ClustalW

1.7

General purpose multiple sequence alignment program for DNA or proteins

ClustalW

COBRAPy

20140530 (default)

COBRApy is a package for constraints-based modeling of biological networks

cobrapy
Cortex_Con0.04c (default)

Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data

cortex
Cortex_Var1.0.5.21 (default)

 A tool for genome assembly and variation analysis from sequence data

cortexVar

cudaMEME

3.0.12 (default)

The GPU version of the MEME motif discovery tool.

cudaMEME

Curtain

0.2.1

Java wrapper for Velvet and Maq - reduces memory footprint of assembly ops.

curtain

cutadapt

1.4.1 (default), 1.2.1, 1.1

cutadapt removes adapter sequences from high-throughput sequencing data.

cutadapt

Cufflinks

2.2.1 (default), 2.2.0, 2.1.1, 2.0.0 (beta), 1.3.0, 1.1.0

Transcript assembly, differential expression, and differential regulation for RNA-Seq

cufflinks

DendroPy

3.12.0

Provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc.

DendroPy

DETONATE

1.8.1 (default), 20140123

DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

DETONATE

DIAL

2010.07.13

De novo Identification of Alleles is a collection of programs to automate the discovery of alleles for a species where we lack a reference sequence  ILLUMINA DATA ONLY.  DOES NOT WORK WITH ROCHE 454.

DIAL

diffReps

1.55.1 (default)

A perl based application that compares the differential enrichment of a histone mark or transcription factor between two contrasting conditions, such as disease vs. control

diffReps

Distruct1.1 (default)
A program for the graphical display of population structure
distruct

DIYABC

0.7.2 (default), 1.0.4.37

Bayesian computation inference on population history using molecular markers

DIYABC

eaUtils

1.1.2-537

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

eaUtils

ESTScan3.0.3 (default)Detects coding regions in DNA sequences, even if they are of low quality, and detects/corrects sequencing errors that lead to frameshifts.ESTScan

ETE2

2.2.r1019

A Python environment for phylogenetic tree exploration.

ETE2

Exonerate

2.2.0

A generic tool for pairwise sequence comparison.

MAKER

fasta36

36.3.6d (default)

Improved tools for biosequence analysis fasta36 
FastQC0.11.2 (default)

A quality control tool for high throughput sequence data

FastQC

fastPHASE

1.4.0

Haplotype reconstruction and estimating missing genotypes from population data.

fastPHASE

Fastx Toolkit

0.0.13

A collection of command line tools for short-read FASTA/FASTQ processing

FASTX

FFPred220130911 (default)Eukaryotic Function Prediction.FFPred2

Foldalign

2.1.1

RNA structure and sequence alignment

Foldalign

freebayes

20140521 (default), 20130417

Bayesian haplotype-based polymorphism discovery and genotyping

freebayes

GAAS0.17 (default)A bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.GAAS
GARM0.7.3 (default)Genome Assembly, Reconciliation and Merging (GARM) is a pipeline of several scripts to combine results from different genome assembliesGARM
GATK3.2.2, 3.1.1 (default), 2.7.2, 2.5.2, 2.2.16Broad Institute tool set for analyzing NGS data for variant discovery and genotyping.GATK
Gblastn2.28 (default)GPU version of NCBI BLAST, with gpu-acceleration for blastn
Equivalent to BLAST+ 2.28.
See gpu benchmarking results for more information.
Gblastn
GEMMA0.94 (default)

Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for GWAS.

GEMMA

geneid

1.4.4

A program to predict genes in anonymous genomic sequences designed with a hierarchical structure.

geneid

GenomeTools1.5.4 (default), 1.5.3, 1.5.1, 1.4.1

A collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named 'libgenometools' which consists of several modules.

GenomeTools

Glimmer

3.02

Glimmer is a system for finding genes in microbial DNA.

glimmer

GMAP/GSNAP

20130714 (default), 20130331, 20120421, 20111120

A Genomic Mapping and Alignment Program for mRNA and EST Sequences  (LARGE GENOME VERSION AVAILABLE AS GMAP/20130331.large)

GMAP

gpuBLAST

1.1 (default) 

The GPU version of NCBI BLAST+. Protein searches (blastp) about 3 times faster than regular BLAST.
Equivalent to BLAST+ 2.2.26.  See gpu benchmarking results for more information.

gpuBLAST

HMMER

3.0

Searches sequence databases for homologs of protein sequences

HMMER

HOMER

4.5 (default), 20130715

NGS analysis toolkit with motif discovery

HOMER

HyPhy20141209 (default)Hypothesis testing using phylogenies`HyPhy
IDBAUD1.1.1 (default), 1.1.0A iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing DepthIDBAUD
IGVTools2.3.26 (default)The igvtools utility provides a set of tools for pre-processing data filesIGVTools

IMa2

8.26.11

Isolation with Migration model for genetic data

ima2

Infernal

1.0.2

For searching DNA sequence databases for RNA structure and sequence similarities.

infernal

IPRSCAN5.7.48.0 (default), 5.6.48.0, 5.4.47.0, 5.1.44.0InterPro is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.iprscan
Jellyfish1.1.4 (default)

Fast memory efficient counting of kmers.

jellyfish
Jellyfish22.1.1 (default)

Fast memory efficient counting of kmers. Jellyfish2 has several enhancements of Jellyfish, and supports longer kmer sizes and better memory management.

jellyfish2

Khmer

1.4 (default), 1.3, 1.2, 1.1, 1.0.1, 0.8.3, 0.8, 0.7.1, 0.6.1

In-memory k-mer counting

khmer

LASTZ

1.02.00

Aligns DNA sequences using pairwise alignment

LASTZ

libSBML5.10.0 (default)

A programming library to help you read, write, manipulate, translate, and validate SBML files and data streams

libSBML

LOX

1.5 (default), 1.4

Inferring level of expression from diverse methods of census sequencing

LOX

MACS

1.3.7

Model-based Analysis of ChIP-Seq (MACS), for identifying transcription factor binding sites.

MACS

MAFFT7.215 (default), 6.864 

MAFFT is a multiple sequence alignment program that offers a range of methods like L-INS-ik, FFT-NS-2, etc.

MAFFT

MAKER

2.31.8 (default), 2.31, 2.28, 2.10

Allows genome projects to independently annotate their genomes and to create genome databases.

MAKER

MaSuRCA2.3.0 (default)

A whole genome assembler that combines de Brujin graph and OLC approaches

MaSuRCA

MAQ

0.7.1

Mapping and assembly qualities.

MAQ

Maqview

0.2.5

A graphical read alignment viewer, specifically designed for the MAQ alignment file.

maqview

MDscan

2004 (default)

A motif-finding application for ChIP-ChIP targets

MDscan

Megan55.8.1 (default)MEtaGenome ANalyzerMegan5

Meme

4.9.1 (default), 4.7.0, 4.4.0

Motif-based sequence analysis tools

MEME

MetaSim

0.9.5

Generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets.

MetaSim

MetaVelvet1.2.02 (default)A short read assember for metagenomics,MetaVelvet

Migrate-n

3.1.6

A bioinformatics tool for estimating population sizes and gene flow

migrateN

MIRA

3.9.18 (beta), 3.4.0 (default)

Sequence assembler for whole genome shotgun and EST sequencing data

MIRA

miRDeep2

0.0.5

Discovers microRNA genes by analyzing sequenced RNAs

miRDeep2

MISO

0.5.2 (default), 0.4.9, 0.4.8, 0.4.7

Probabilistic analysis and design of RNA-Seq experiments for identifying isoform regulation

MISO

Mothur

1.33.2 (default), 1.33.2b, 1.33.0, 1.33.0b, 1.31.2, 1.31.2b, 1.30.1, 1.29.0, 1.27.0, 1.26.0, 1.25.0, 1.24.1, 1.24.0, 1.23.1, 1.21.1, 1.20.3, 1.18.0

A bioinformatics tool kit for microbiologists. MPI support.
non-MPI versions (multi-threaded, single node) have a "b" suffix on the module number (e.g., 1.33.2b) 

mothur

mpiBLAST

1.6.0

The MPI version of the Basic Local Alignment Search Tool

mpiBLAST

MPI-PHYLIP20101115The MPI version of the PHYLIP phylogeney package.MPI-PHYLIP

MrBayes

3.2.1

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. Uses BeagleLib

MrBayes

MREPS

2.5

A flexible and efficient software for identifying serial repeats (usually called tandem repeats) in DNA sequences.

mreps

MUMmer

3.22

A system for rapidly aligning entire genomes, whether in complete or draft form

MUMmer

Newbler2.9 (default)De novo sequence assembler from Roche/454newbler

NGSUtils

0.5.0c

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

NGSUtils

Oases

0.2.08 (default), 0.2.07, 0.1.22

De novo transcriptome assembler for short reads

oases

OpenBUGS

3.2.1

BUGS is a software package for performing Bayesian inference Using Gibbs Sampling

OpenBUGS

PAML

4.4c

Tools for phylogenetic analyses of DNA or protein sequences using maximum likelihood

paml

pandaseq

20150212 (default), 20130611

 PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence. pandaseq
PBSuite14.7.14 (default), 14.6.24Software for Long-Read Sequencing Data from PacBio - includes PBJelly (Jelly.py)PBSuite
PeakRanger1.18 (default)A multi-purporse software suite for analyzing next-generation sequencing (NGS) data.PeakRanger

PeakSeq

1.1 (default)

PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments using mapped reads

PeakSeq

pfilt1.5 (default)

pfilt is designed to mask out regions of low-complexity, coiled-coil regions and more regions w/ extremely biased amino acid compositions. Masking replaces amino acid characters with X's

pfilt
PGDSpider2.0.7.0 (default)An automated data conversion tool for connecting population genetics and genomics programsPGDSpider

PHYLIP

3.5

A computational packages used for inferring phylogenies

PHYLIP

PhyML

20120412, 3.0 (default)

For phylogenetic tree development

PhyML

picardTools

1.113 (default), 1.89

Command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files

picardTools

PICRUSt1.0.0 (default)A bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomesPICRUSt

PILER

1.0

A package for genomic repeat analysis.

piler

plink

1.07

A whole genome association analysis toolset for the analysis of genotype/phenotype data.

plink

PRANK

111130

A probabilistic multiple alignment program for DNA, codon and amino-acid sequences

PRANK

PRESTO1.0.1 (default)PRESTO is optimized software for permutation testing and for computing empirical distributions of order statistics via permutationPRESTO

PROBCONS

1.12

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

PROBCONS

QIIME

1.8.0, 1.7.0, 1.4.0 (default)

QIIME is a pipeline application that takes raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis and visualization.

QIIME

QualiMap2.0 (default) Provides quality control of alignment sequencing data and its derivatives like feature countsQualiMap
QUAST2.3 (default)

The tool evaluates genome assemblies by computing various metrics

QUAST

QuEST

2.5

Statistical software for analysis of ChIP-Seq data with data and analysis results visualization via the USSC Genome Browser

QuEST

Ray2.3.1 (default), 2.0.0A parallel de novo genome assemblerRay
raxml8.0.6 (default), 7.7.8, 7.3.0, 7.2.6RAxML is a fast implementation of maximum-likelihood (ML) phylogeny estimation that operates on both nucleotide and protein sequence alignments. raxml
RealPhy1.09 (default)The Reference sequence Alignment based Phylogeny builder RealPhy
REAPR1.0.17 (default)

A tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison

REAPR

RECON

1.07 (default), 1.05

A package for automated de novo identification of repeat families from genomic sequences.

recon

RepeatScout

1.05

A tool to discover repetitive substrings in DNA

RepeatScout

RepeatModeler

1.0.7 (default), 1.0.5

A de-novo repeat family identification and modeling package

RepeatModeler

RepeatMasker

4.0.0 (default), 3.3.0, 3.2.9

Screens DNA sequences for interspersed repeats and low complexity DNA sequences.

RepeatMasker (4.0.0)

RMBlast

2.2.28 (default), 2.2.27, 1.2

A RepeatMasker compatible version of the standard NCBI BLAST suite

RMBlast

RSEM

1.2.19 (default), 1.2.11, 1.2.10, 1.2.0, 1.1.20, 1.1.13

A software package for estimating gene and isoform expression levels from RNA-Seq data

RSEM

rtax

0.983 (default), 0.981

Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene

rtax

ruffus2.2 (default)

Ruffus is a lightweight python module for running computational pipelines

ruffus

SAMStat

20130521 (default)

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format

SAMStat

SAMtools

1.0, 0.1.19 (default), 0.1.18, 0.1.12a

Various utilities for manipulating SAM (Sequence Alignment/Map) format for storing large nucleotide sequence alignments

SAMTools

SGA0.10.13 (default)

SGA is a memory efficient de novo genome assembler based on the concept of string graphs

SGA
SHORE0.9.0 (default)Analysis suite for Illumina short read data. SHORE
SHOREmap2.1 (default)SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants. SHOREmap

Sickle

1.210

A windowed adaptive trimming tool for FASTQ files using quality

sickle

SLIDE

3.4

Screening for Ligands by Induced-fit Docking, Efficiently

SLIDE

SLOPE20140114 (default)

Finds the best split-read alignments to the reference genome, and clusters and outputs alignments.

SLOPE

Snap

2006-07-28

A gene prediction program.

MAKER

SnpEff4.0e (default), 3.3e

A variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants.

SnpEff
SNPhylo

20140701 (default)

A pipeline to generate a phylogenetic tree from huge SNP data

SNPhylo

SOAP

1.11

Short Oligionucleotide Alignment Program

SOAP

SOAP2

2.21

Short oligonucleotide alignment, redesigned version of Soap1 for large data sets.

SOAP2

SOAP.Coverage

2.7.7

Calculates sequencing or physical coverage, duplication rate and block details for segments and whole genomes.

SOAPcoverage

SOAPdenovo

1.05 (default)

A novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads.

SOAPdenovo

SOAPdenovo2

r224 (default)

A novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads.

SOAPdenovo2

SOAPdenovoTrans1.04 (default)

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts

SOAPdenovoTrans
SOAPindel2.1 (default), 1.1Calls  indels from the next-generation paired-end sequencing data.SOAPindel

SOAPsnp

1.02

A sequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference.

SOAPsnp

SOAPsv1.02 (default)A program for detecting the structural variation by whole genome de novo assembly System Requirements.SOAPsv

SomaticSniper

20140604 (default)

Identifies SNPs that are different between tumor and normal (or in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences

SomaticSniper

SOPRA

1.4.6

Contig scaffolding assembler for mate pair/paired-end reads from Illumina and SOLiD platforms

SOPRA

SPAdes3.1.1 (default, GCC 4.7.1), 3.0.0

A genome assembler intended for both standard isolates and single-cell MDA bacteria assemblies

SPAdes

SRAToolkit

2.1.6

Tools for manipulating NCBI Sequence Read Archive (SRA) files.

SRAToolkit

SSAKE

3.8

Assembles millions of very short DNA sequences

SSAKE

Stacks

0.998

A software pipeline for building loci out of a set of short-read sequenced samples

stacks

STAMP

2.0.2 (default), 2.0

Statistical Analysis of Metagenomic Profiles - used for analyzing metagenomic profiles.

STAMP

Stampy1.0.23 (default)

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome

Stampy
STAR

2.3.0e (default)

STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays

STAR
Structure2.3.4 (default)Uses multi-locus genotype data to investigate population structure.structure
SVDetect0.8b (default)A tool to detect genomic structural variations from paired-end and mate-pair sequencing dataSVDetect

tabix

0.2.6

Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.

tabix

Tablet

1.12.03.26

A high performance assembly visualization tool written in Java.

Tablet

TAMO

1.0

A Python application for analyzing transcriptional regulation using DNA-sequence motifs.

TAMO

tcoffee

9.01

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures

tcoffee

TMHMM2.0c (default)Prediction of transmembrane helices in proteinsTMHMM

Tophat

1.4.1 (default),1.3.1, 1.2.0

A fast splice junction mapper for RNA-Seq reads.

TopHat

Tophat22.0.12 (default), 2.0.11, 2.0.8b, 2.0.5, 2.0.4, 2.0.0 (beta)A fast splice junction mapper for RNA-Seq reads.TopHat2
TransABySS1.4.8 (default)

A  software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data

TransABySS
TransDecoder2.0.1 (default), 20140116Identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.TransDecoder
Tree-Puzzle5.2 (default) Maximum likelihood analysis for nucleotide, amino acid, and two-state datatreePuzzle

TRF

4.04

A program to locate and display tandem repeats in DNA sequences.

trf

Trim Galore!0.3.3 (default)A FastQC and cutadapt wrapper used for adapter removal and quality trimmingTrimGalore
Trimmomatic0.32 (default), 0.30A flexible read trimming tool for Illumina NGS dataTrimmomatic
Trinotate20140708 (default)A comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organismsTrinotate

Trinity

20140413p1 (default), 20130225, 20130108, 20120608, 20111029, 20110820

A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.

trinity

Ugene

1.11.0 (default), 1.9.0

A multifaceted genome analysis suite

ugene

USEARCH

6.0.307 (default), 6.0.152, 5.2.32, 5.2.236

Fast sequence analysis and search tool, similar to BLAST.

USEARCH

VarScan2.3.6 (default)VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing dataVarScan
VCFTools0.1.12a (default), 0.1.9, 0.1.8bDesigned for working with VCF files, such as those generated by the 1000 Genomes Project.vcftools

Velvet

1.2.07 (default), 1.2.07, 1.1.05, 1.1.01

Popular sequence assembler for very short reads. 1.1.01 has MPI support.

velvet

Vmatch

2.2.0 (default)

A tool for efficiently solving large scale sequence matching tasks. For access CONTACT THE HPCC.

*More Info.

WebLogo

2.8.2

Easy motif creation - used to support HOMER but can be used standalone with seqlogo

WebLogo

wgscelera8.2 (default), 8.1, 7.0, 6.1

A de novo whole-genome shotgun (WGS) DNA sequence assembler.

 

WISE2

2.2.3rc7 (default), 2.1.20c

Compares DNA sequences at level of its protein translation, to allow simultaneous prediction of say gene structure with homology based alignments.

wise2