name | ver | description | note | tested on | webpage | depend on |
abyss-mpi | 1.9.0 | ABySS assembler (MPI) | | RHEL 6.4 | link | sparsehash |
abyss | 1.5.1 | ABySS assembler (Non-MPI) | | CentOS 6.2 | link | |
ack | 2.12 | ack: a tool like grep, optimized for programmers | | | link | |
allpaths-lg | 48744 | ALLPATHS-LG Genome Assembler | | CentOS 6.4 | link | gcc4.7+ |
amos | 3.1.0 | AMOS is a collection of tools and class interfaces for the assembly of DNA reads. | | SL6.1 | link | |
ant | 1.9.6 | ant | | CentOS 6.6 | link | |
arachne | 3.2_March9_2009 | Arachne assembler | | SL6.1 | link | |
asciiplots | | ASCII plot | | CentOS 6.5 | link | |
aspera-connect-client | 3.3.3.81344 | Aspera Connect Client (commercial; only client is available free of charge; Linux; x86_64) | | CentOS 6.3 | link | |
augustus | 3.0.2 | gene prediction program Augustus | | RHEL 6.1 | link | boost |
autossh | 1.4c | autossh | | | link | |
bam2fastq | 1.1.0 | The BAM format is an efficient method for storing and sharing data from modern, highly parallel sequencers. While primarily used for storing alignment information, BAMs can (and frequently do) store unaligned reads as well. | | SL6.1 | link | |
bamtools | | BAMtools is a project that provides both a C++ API and a command-line toolkit for reading, | | SL6.1 | link | cmake |
bedtools | 2.18.1 | BEDTools is an extensive suite of utilities for comparing genomic features in BED format. | | CentOS 6.4 | link | |
bfast | 0.7.0 | BFAST Blat-like Fast Accurate Search Tool | | SL6.1 | link | |
bioawk | | BioAwk | | CentOS 6.4 | link | |
biopython | 1.56 | BioPython | | SL6.1 | link | |
biotoolbox | 1.12.3 | biotoolbox | | CentOS 6.4 | link | |
blasr | | BLASR Basic Local Alignment with Successive Refinement | | CentOS 6.6,RHEL6.1 | link | hdf5 |
blast+ | 2.2.31+ | NCBI BLAST+ | | CentOS 6.4 | link | |
blast | 2.2.26 | Legacy NCBI BLAST | | CentOS 6.4 | link | |
blat | 3.5 | BLAT | | SL6.1 | link | |
boost-with-mpi | 1.49.0 | Boost library with Boost.MPI (for C++) | | SL6.1 | link | |
boost | 1.58.0 | Boost library (for C++) | | RHEL6.4 | link | |
bowtie | 1.0.0 | bowtie | | SL6.1 | link | |
bowtie2 | 2.2.5 | bowtie2 | | CentOS 6.6 | link | |
bsmap | 2.5 | bsmap Bisulfite Sequence Mapping Program | | SL6.1 | link | |
bwa-mem | 0.7.10 | Burrows-Wheeler Aligner (BWA) Latest version with bwa-mem (still unstable?). | | CentOS 6.4 | link | |
bwa | 0.6.2 | Burrows-Wheeler Aligner (BWA) Recommended stable version for sampe. | | CentOS6.4 | link | |
cabog | 7.0 | CABOG is scientific software for biological research. | | SL6.1 | link | |
cegma | v2.4.010312 | CEGMA - Core Eukaryotic Genes Mapping Approach | | RHEL6.1 | link | |
centroidfold | 0.0.10 | Centroidfold | | | link | |
chapel | 1.8.0 | Chapel: Parallel Programming Language | | RHEL 6.3 | link | |
cmake | 2.8.12.2 | CMake the cross-platform, open-source build system. | | SL6.1 | link | |
compiler-envs | 1.3 | Set environmental variables for compilers. | | SL6.1 | link | |
cpas | 1.09 | cpas (CPp As a Script) | | SL6.1 | link | |
cppunit | 1.12.1 | CppUnit | | SL6.3 | link | |
ctags | 5.8 | Excuberant ctags | | | link | |
cufflinks | 2.2.1 | Cufflinks Transcript assembly, differential expression, and differential regulation for RNA-Seq | | SL6.1 | link | |
dictd | 1.11.2 | dictd | | SL6.1 | link | |
dindel | 1.01 | Dindel is a program for calling small indels from short-read sequence data | | SL6.1 | link | |
dwgsim | 0.1.10 | dwgsim | | CentOS 6.4 | link | |
eutils | 2012Aug08 | E-utilities for NCBI Entrez Direct | | CentOS 6.4 | link | |
exonerate | 2.2.0 | Exonerate | | CentOS 6.4 | link | |
expat | 2.1.0 | expat | | SL6.1 | link | |
fastqc | 0.10.0 | FastQC | | SL6.1 | link | |
fastx-toolkit | 0.0.13.2 | fastx-toolkit | | SL6.1 | link | libgtextutils |
freeglut | 2.8.1 | FreeGLUT | | | link | |
gcc | 4.9.0 | GCC (latest stable) | | CentOS 6.5 | link | gmp mpc mpfr |
gcc47 | 4.7.3 | GCC 4.7.3 | | CentOS 6.4 | link | gmp mpc mpfr |
gcc48 | 4.8.2 | GCC 4.8.2 | | CentOS 6.4 | link | gmp mpc mpfr |
geneid | 1.4.4 | geneid: a program to predict genes in genomic sequences | | RedHat 6.1 | link | |
ghc | 7.8.3 | GHC The Glasgow Haskell Compiler | | SL6.1 | link | |
git | 2.4.6 | git | | Cent OS 6.4 | link | autotools |
glances | | a system monitoring tool (works on curses) | | | link | python |
gmp | 5.1.2 | GMP (The GNU Multiple Precision Arithmetic Library) | | CentOS 6.4 | link | |
gnuparallel | 20140322 | GNU parallel | | CentOS 6.4 | link | |
gsl | 1.16 | GSL GNU Scientific Library | | CentOS 6.4 | link | |
gtest | 1.6.0 | Google Test | | | link | |
haskellplatform | 2014.2.0.0 | Haskell Platform | | CentOS 6.4 | link | ghc-7.8.3 |
hdf5 | 1.8.15-patch1 | HDF5 Hierarchical Data Format | | CentOS 6.6,RHEL6.1 | link | |
hgap | 1.4 | HGAP: Hierarchical Genome Assembly Process | | SL6.3 | link | |
hitec | 1.0.2 | HiTeC high-throughput sequencing data, such as those generated by the Illumina Genome Analyzer. | | SL6.1 | link | |
hmmer3 | 3.1b1 | HMMER - biosequence analysis using profile hidden Markov models | | | link | |
idba-ud | 1.1.1 | Iterative De Bruijn graph de novo assembler for short reads with highly Uneven Depth | | CentOS 6.4 | link | |
idba | 1.1.1 | Iterative De Bruijn graph Assembler | | CentOS 6.4 | link | |
igv | 2.3.14 | Integrative Genomics Viewer | | CentOS 6.4 | link | |
igvtools | 2.3.14 | Integrative Genomics Viewer Tools | | CentOS 6.4 | link | |
javahome_rhel | 1.0 | Set up JAVA_HOME for RedHat Enterprise Linux (or equivalents) | | RHEL6.4 | link | java-1.x.0-openjdk-devel |
javalib | 1.0 | Set up CLASSPATH for Java libraries | | SL6.1 | link | |
jellyfish | 1.1.11 | JELLYFISH - Fast, Parallel k-mer Counting for DNA (Version 1.1.11) | | CentOS6.4 | link | |
jq | 1.3 | ./jq | | CentOS 6.4 | link | |
klab | | klab: Kasahara lab. public repository (mostly for various bioinformatics tools) | | CentOS6.3 | link | |
lapack | 3.4.2 | LAPAK is a library of Fortran 90 with subroutines for solving | | SL6.1 | link | |
last | 418 | LAST finds similar regions between sequences. | | CentOS 6.4 | link | |
ldc2 | 0.14.0 | LDC - the LLVM-based D compiler | | Ubuntu 12 | link | |
lftp | 4.4.9 | lftp | | | link | |
libbz2 | 1.0.6 | bzlib (bzip2) | | | link | |
libevent | 2.0.21 | libevent | | CentOS 6.4 | link | |
libgtextutils | 0.6 | libgtextutils | | | link | |
libmaa | 1.2.0 | libmaa | | | link | |
lua | 5.3.1 | Lua | | CentOS 6.4 | link | |
lua51 | 5.1.5 | Lua 5.1.x | | CentOS 6.4 | link | |
luajit | 2.0.4 | LuaJIT | | CentOS 6.4 | link | |
macs | | MACS | | CentOS6.4 | link | |
mafft | 7.058 | Multiple alignment program for amino acid or nucleotide sequences | | CentOS 6.4 | link | |
masurca | 2.0.3.1 | MaSuRCA assembler | | | link | |
matplotlib | 1.4.3 | matplotlib: a python 2D plotting library | | CentOS 6.4 | link | |
maven | 3.1.1 | maven | | | link | |
mpc | 1.0.1 | MPC | | | link | |
mpfr | 3.1.2 | GNU MPFR Library | | CentOS 6.4 | link | |
mpio | | mpio library | | CentOS 6.4 | link | |
msgpack-rpc | 0.3.1 | Message Pack RPC for C++ | | | link | mpio |
msgpack | | Message Pack for C++ | | | link | |
mummer | 3.23 | MUMmer (alignment program using Suffix Tree) | | CentOS6.4 | link | |
muscle | 3.8.31 | MUSCLE: Multiple Alignment Program | | CentOS 6.4 | link | |
musica2 | 2.1.1 | MuSICA2 | | | link | |
mysql | 5.6 | MySQL | | CentOS 6.1 | link | cmake |
ncbigenome | 2.7.6 | NCBI Genome Workbench | | | link | |
netcat | 0.7.1 | netcat | | | link | |
nextclip | | NextClip: Clip and analyse Illumina Nextera Long Mate Pair reads | | CentOS6.6 | link | |
ngsutils | | NGSUtils: Tools for next-generation sequencing analysis | | CentOS6.6 | link | |
novoalign | 3.02.02 | Sensitive sequence aligner (commercial; Linux 2.6; x86_64) | | CentOS 6.4 | link | |
oases | 0.2.08 | Oases is a de novo transcriptome assembler designed to | | SL6.1 | link | |
ocaml | 4.02 | OCaml | | | link | |
onlinecall | 0 | Online Call | | SL6.1 | link | |
pacbiotoca | 7.0 | PacBioToCA | | CentOS 6.3 | link | |
pbjelly | 14.9.9 | PBJelly: Gap closure tool for PacBio long reads (renamed to pbsuite) | | | link | |
pbsim | 1.0.3 | PBSim: Read simulator for PacBio RS | | | link | |
pbsuite | 14.9.9 | Analysis tool for PacBio Long Reads | | RHEL 6.5 | link | |
pbzip2 | 1.1.6 | pbzip2 | | | link | |
pear | 0.9.6 | PEAR: Paired-end read merger | | CentOS6.6 | link | |
peassembler | 1.2 | PE-Assembler | | | link | |
pfi-common | | pfi-common: General Purpose C++ library for GCC 4.1.2 and later | | SL6.1 | link | |
picard | 1.129 | Picard (SAM manipulation) | | CentOS 6.6 | link | |
pigz | 2.3 | pigz | | CentOS 6.4 | link | |
pkgconfig | 0.28 | pkg-config | | SL6.1 | link | |
plantuml | 7986 | PlantUML | | | link | |
platanus | 1.2.1 | Platanus genome assembler | | CentOS 6.6 | link | |
porg | 0.6 | Porg (Package organizer) | | | link | |
pv | 1.5.7 | Pipe Viewer: a terminal-based tool for monitoring the progress of data through a pipeline | | | link | |
pysam | 0.7.5 | pysam | | CentOS 6.4 | link | |
python-setuptools | 0.6c11 | python setuptools | | | link | python |
python | 2.7.6 | Python (2.x) | | | link | |
python3 | 3.4.0 | python3 (3.x) | | CentOS 6.5 | link | |
quast | 2.3 | QUAST: Quality Assessment Tool for Genome Assemblies | | CentOS 6.6 | link | matplotlib |
R | 3 | R language for statistical computing |
| CentOS 6.5 | link | |
recon | 1.07 | RECON: a package for automated de novo identification of repeat families from genomic sequences | | | link | |
repeatmasker | open-4-0-3 | RepeatMasker | | | link | recon, trf, rmblast |
repeatmodeler | open-1-0-7 | RepeatModeler to prepare species specific database for RepeatMasker | | RHEL6.4 | link | RepeatMasker & Libraries, RECON, RepeatScout, TRF, rmblast |
rlwrap | 0.37 | rlwrap is a wrapper that uses the GNU readline library to allow the editing of keyboard input for any other command. | | CentOS6.4 | link | readline |
rmblastn | 2.2.28 | RMBlast - A modified version of NCBI Blast for use with RepeatMasker and RepeatModeler | | CentOS 6.4 | link | |
rsem | 1.2.18 | RNA-Seq by Expectation-Maximization | | | link | |
ruby | 2.2.2 | Ruby (2.x) | | | link | |
ruby19 | 1.9.3-p545 | Ruby (1.9.x) | | | link | |
samtools-dylib | 0.1.17 | samtools (Shared library. libbam) | | | link | |
samtools | 0.1.19 | samtools | | RHEL 6.1 | link | |
seqtk | | seqtk | | CentOS 6.5 | link | |
sga | | SGA is a de novo genome assembler based on the concept of string graphs. | | SL6.1 | link | google-sparsehash bamtools |
smlnj | 110.78 | Standard ML of New Jersey (abbreviated SML/NJ) is a compiler | | CentOS6.5 | link | |
smrtanalysis-centos | 2.3.0.140936.p2 | PacBio SMRT Analysis Pipeline (CentOS binary) | | CentOS 6.6 | link | wget |
snappy | 1.1.1 | Snappy (a fast compressor/decompressor) | | | link | |
soap-anotherec | unknown | SOAP ErrorCorrection: Another read correction package | | CentOS 6.4 | link | |
soap3gpu | 0.01 | SOAP3-The alignment program in this package is optimized to work for multi-millions of short reads each time by running a multi-core CPU and the GPU concurrently. | | SL6.1 | link | |
soapdenovo-prepare | 2.0 | SOAPdenovo-prepare | | | link | |
soapdenovo | 240 | SOAPdenovo2 (up to 127mer) | | CentOS 6.4 | link | |
soapec | 2.01 | SOAPec: Read correction package designed to correct Illumina short reads. | | CentOS 6.4 | link | |
soapgapcloser | 1.12-r6 | SOAP GapCloser: Gap closing tool using the abundant pairs of short reads | | CentOS 6.4 | link | |
sparsehash | 2.0.2 | sparsehash An extremely memory-efficient hash_map implementation | | SL6.1 | link | |
sprai | 0.9.9.7 | Sequencing error correction tool for long reads such as PacBio CLR | | | link | |
sratoolkit | 2.5.2 | SRAToolkit (for CentOS & Mac) | | CentOS 6.6 | link | |
stacks | 1.35 | Stacks: Genetic map builder for RAD sequencing | | CentOS 6.4 | link | |
tcc | 0.9.25 | tcc (Tiny C Compiler) | | | link | |
texlive | 20120411 | ptexlive | | SL6.1 | link | |
tgew | | Tiny Grid Engine Wrapper | | CentOS6.3 | link | |
thrift | 0.2.0 | Thrift (wo/ruby, w/boost) | | | link | |
tig | 2.0.3 | tig (CUI-based git browser) | | | link | |
tophat | | TopHat is a fast splice junction mapper for RNA-Seq reads. | | CentOS 6.6 | link | |
trans-abyss | | Trans-ABySS | | | link | |
transdecoder | r20131117 | TransDecoder (Find Coding Regions Within Transcripts) | | RHEL 6.1 | link | |
trf | 4.07b | Tandem Repeats Finder | | | link | |
trimmomatic | 0.33 | Trimmomatic: java based Illumina sequence trimming tool | | CentOS 6.6 | link | |
trinity | 20131110 | RNA-Seq De novo Assembly Using Trinity | | RHEL 6.4 | link | |
trinity2 | 2.0.6 | RNA-Seq De novo Assembly Using Trinity | | CentOS 6.6 | link | |
ttyrec | 1.0.8 | ttyrec (TTY RECorder) | | | link | |
ucscuserapps | | UCSC genome browser related tools | | CentOS6.6 | link | |
udr | | UDR: UDT-enabled rsync | | | link | |
udt | 4.11 | UDP file transfer library | | | link | |
utgb | 1.5.9 | UT Genome Browser | | | link | |
velvet | 1.2.10 | velvet assembler | | CentOS 6.6 | link | |
viennarna | 2.1.5 | viennarna | | | link | |
vim | 7.4 | Vim | | CentOS 6.4 | link | python (if you enable python), ruby (if you enable ruby), lua51 (if you enable lua or luajit), luajit (if you enable luajit) |
virtualenv | | virtualenv (for Python) | | CentOS6.4 | link | |
wget | 1.16.3 | Wget | | OS X Yosemite | link | |
wgs | 8.1 | Celera Assembler 8.1 | | RHEL 6.4 | link | |
wise | 2.4.1 | genewise is the homology based gene prediction program | | | link | |
x10 | 2.5.3 | X10 lang | | CentOS 6.1 | link | |
xerces2 | 2.8.0 | Xerces C++ 2 (XML Parser) | | | link | |
zlib | 1.2.8 | zlib | | CentOS 6.4 | link | |
zsh-lpm-comp | 1.0 | Set zsh autocompletion for LPM | | CentOS 6.4 | link | |
zsh-util-envs | 1.1 | Set environmental variables and define utility functions for zsh | | SL6.1 | link | |