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spades

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines

Versions:3.9.0; 3.10.0; 3.12.0
License:GPLv3
Categories:bioinformatics
sparsehash

The Google SparseHash project contains several hash-map implementations in use at Google, with different performance characteristics, including an implementation that optimizes for space and one that optimizes for speed.

Versions:2.0.3
License:https://raw.githubusercontent.com/sparsehash/sparsehash/master/COPYING
Categories:Programming, library
spglib

Spglib is a library for finding and handling crystal symmetries written in C.

Versions:1.9.8
License:New BSD
Categories:crystal symmetries, k-points
spparks

sppakrs is a Monte Carlo program.

Versions:18May17
License:http://spparks.sandia.gov/open_source.html
Categories:Monte Carlo, crystal symmetries
sratoolkit

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

Versions:2.8.2-1; 2.7.0; 2.9.6
License:GPLv2
Categories:bioinformatics
stacks

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.

Versions:2.1; 1.35; 2.3e; 1.41; 1.45
License:GNU GPL v3
Categories:Genomics, Pipeline, phylogenetics
stampy

a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Versions:1.0.32
License:GPLv2
Categories:bioinformatics
star

Spliced Transcripts Alignment to a Reference

Versions:2.5.2a
License:GPLv3
Categories:bioinformatics
starccm

Star-CCM+ is a CFD application that supports parallel processing.

Versions:12.00.000-R8; 11.04.010; 11.04.010-R8; 13.04.010; 12.04.010-R8; 12.04.010; 13.04.010-R8
License:CFD
Categories:
stata

Statistical analysis software.

Versions:16; 14; 15
License:http://www.stata.com/order/end-user-license-agreement/
Categories:econometrics, statistics
stata-mp

Statistical analysis software.

Versions:16; 14; 15
License:http://www.stata.com/order/end-user-license-agreement/
Categories:econometrics, statistics
strelka

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

Versions:1.0.15
License:GPLv3
Categories:bioinformatics
stringtie

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Versions:1.3.3b; 1.2.4
License:Artistic 2.0
Categories:bioinformatics
subread

a tool kit for processing next-gen sequencing data

Versions:1.6.1; 1.5.0
License:GPLv2
Categories:bioinformatics
subversion

Apache Subversion centralized version control system.

Versions:1.10.0-1
License:https://www.apache.org/licenses/LICENSE-2.0
Categories:SVN, reversion control, version control
swig

SWIG is an interface compiler.

Versions:3.0.10
License:http://www.swig.org/legal.html
Categories:Compiler, Programming
szip

Szip is a compression library used with HDF5.

Versions:2.1
License:https://www.hdfgroup.org/doc_resource/SZIP/
Categories:Utility, compression
tabix

A useful tool that indexes large .vcf files

Versions:0.2.6
License:GPLv2
Categories:bioinformatics
taco

Multi-sample transcriptome assembly from RNA-Seq

Versions:0.5.1
License:http://tacorna.github.io/#license
Categories:Application, Biostatistics, python
tax2tree

The tax2tree software package was developed in collaboration with Greengenes for the purpose of transferring a taxonomy from one tree to another. Specifically, the motivation was to reduce the manual curation effort necessary for each release of Greengenes by automating the decoration of taxonomy.

Versions:1.0
License:Unknown
Categories:
tecplot

Plotting and visualization software that gives full control over 2-D and 3-D plot parameters.

Versions:2016
License:plotting, visualization
Categories:
thermocalc

software package for thermodynamic calculations

Versions:2016a
License:Academic Research license
Categories:thermodynamic
tophat

TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions.

Versions:2.0.9; 2.0.11; 2.0.0
License:GPLv3
Categories:bioinformatics
torch

Torch is a scientific computing framework with wide support for machine learning algorithms.

Versions:170802; 160726
License:https://raw.githubusercontent.com/torch/torch7/master/COPYRIGHT.txt
Categories:CUDA, machine learning
transdecoder

TransDecoder identifies candidate coding regions within transcriptsequences, such as those generated by de novo RNA-Seq transcript assemblyusing Trinity, or constructed based on RNA-Seq alignments to the genomeusing Tophat and Cufflinks.

Versions:5.0.1
License:BSD 3-clause
Categories:bioinformatics sequencing coding transcript
trilinos

Trilinos is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.

Versions:12.8.1; 12.8.1-gcc-5.4.0-openmpi-3.0.0; 12.12.1-gcc-5.4.0-openmpi-1.10.2; .12.8.1 with openmpi/3.0.0 gcc/5.4.0
License:https://trilinos.org/download/license/
Categories:engineering, multi-physics
trimgalore

Consistent quality and adapter trimming for RRBS or standard FastQ files

Versions:0.4.2
License:https://www.gnu.org/licenses/gpl-3.0.en.html
Categories:Perl, Script, bioinformatics
trimmomatic

Trimmomatic: A flexible read trimming tool for Illumina NGS data

Versions:0.36
License:GNU GPL v3
Categories:Sequencing, bioinformatics
trinity

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Versions:2.2.0; 2.4.0; 2.3.2
License:GPLv2
Categories:bioinformatics
twinscan

Twinscan gene-structure prediction

Versions:3.5
License:???
Categories:Genomics, bioinformatics
uclust

UCLUST v1.2.22q (C) Copyright 2009-10 Robert C. Edgar.

Versions:1.2.22q
License:These binaries are licensed only for use in PyNAST and QIIME. The license does not permit stand-alone use.
Categories:
udunits

The UDUNITS-2 package provides support for units of physical quantities.

Versions:2.2.20
Categories:Conversion, Units
unanimity

C++ library and its applications to generate and process accurate consensus sequences

Versions:2.1.0; 2.0.4
License:GPLv2
Categories:bioinformatics
usearch

USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

Versions:8.1
License:GPLv3
Categories:bioinformatics
valet

This software is Open Source. almaBTE is a pipeline for detecting mis-assemblies in metagenomic assemblies.

Versions:1.0
License:https://github.com/marbl/VALET
Categories:Genomics
valgrind

Valgrind is an instrumentation framework for building dynamic analysis tools.

Versions:3.11.0
License:GNU GPL v2
Categories:Instrumentation, Utilities
vasp

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] VASP, The Vienna Ab initio simulation package, a plane wave electronic structure code.

Versions:old-5.3.5.31Mar2014; 5.4.4.18Apr17; 5.4.1.05Feb16.p2.b; 5.4.4.18Apr17.vaspsol.170729; old-5.3.3.18Dec2012; old-5.3.5.31Mar2014wannier90v12; 5.4.4.18Apr17.p1; old-4.6.36Feb09; old-5.2.12.11Nov2011; 5.4.1.05Feb16.p2; old-5.3.2.13Sep2012
License:https://www.vasp.at/index.php/faqs
Categories:electronic structure code, molecular dynamics
vcfanno

Vcfanno provides fast, flexible annotation of genetic variants

Versions:0.1.1-rc2
License:GPLv3
Categories:bioinformatics
vcftools

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

Versions:0.1.14
License:GPLv3
Categories:
velvet

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies such as Solexa or 454.

Versions:1.2.10; 1.2.10-big
License:GNU GPL v2
Categories:Assembly, bioinformatics
Current page: 12
Total pages: 13
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