There are three kind of softwares, the supercomputing software is used through a terminal, with a queue system, you can read the manual at the Picasso documentation section.

The virtual software can be accessed through a virtual desktop, after doing login in this web page you will see a new menu item to access your virtual desktop.

To use the web software you don´t need to have an account, you can access it clicking here.

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Annotation
annotsvv3.1Terminal
annovarv010216v141215v170615Use onlineTerminal
autofactv3.4ManualTerminal
beastv1.1.1v2.4.0ManualTerminal
beast_oldv1.7.5ManualTerminal
brakerv2.1.5Terminal
eggnog-mapperv2.1.6Terminal
genotev0.5b1Terminal
interproscanv5.44.79v5.54.87TerminalAnotación de proteinas
lionv171220Terminal
makerv2.26v2.28v2.31.6v3.01.03ManualTerminal
mothurv1.29.2v1.34.3v1.39.5v1.44.3v1.44.3_sdManualTerminal
phymlv20130513ManualTerminal
prokkav1.12v1.14.5Terminal
scbi_variantsvcurrentTerminalhtml generation
sma3v2v2.1v2.1_perlv2.2Terminal
snappv1.1.1v2.4.0ManualTerminal
snpeffv4.2v4.3v4.4v5eTerminal
trinotatev20130826ManualTerminal
unifamv1.0.0Terminal
vepv95.2Terminal
Chemistry
ABCClusterv2.1Terminal
acidv2.0.1ManualTerminal
adfv2014.07v2016.106ManualTerminal
aromav1.0(default)v1.0_modif_xyvb4ManualTerminal
cp2kv3.0_ssmpManualTerminal
crystalv2.0.1mpiv14_1_0_2v14_1_0_2mpiv14_1_0_3v14_1_0_3mpiv17_intelv17_ompiManualTerminal
daltonv2018_git_mpiv2020_gcc11_mpiUse onlineTerminal//daltonprogram.org/www/citation.html
fhi-aimsv150518v150518_impiv151012v151012_vibv211217ManualTerminalFritz Haber Institute ab initio molecular simulations is an accurate all-electron, full-potential electronic structure code package for computational materials science
gamessv05122014v30092018ManualTerminal
gatev8.2v9.1_gcc7.5.0Terminal
gaussianv09A02v09C01(default)v09C01_pgiv16A03v16A03_21ManualTerminal
molcasv7.8v7.8_ompv8.0v8.0gpuv8.01(default)v8.2v8.2_gfortv8.2_modifv8.2_mpi_modifv8.4v8.4_amd_intelv8.4_completov8.4_nv8.4betav8.4beta_intelManualTerminalMolcas allow an accurate ab initio treatment of very general electronic structure problems for molecular systems
moldenv5.1v7.1Terminal
multiwfnv3.3.6v3.6ManualTerminal
openbabelv2.3.2ManualTerminal
orcav4.0.1v4.1.0v4.1.1v4.2.0v4.2.1v5.0.1v5.0.2v5.0.3ManualTerminal
phonopyv1.14.2ManualTerminal
qchemv4.0.1v4.1.1v4.3.2v4.3.2_ompiv5.3.0v5.3.0_testManualTerminal
quantumespressov5.1v6.5_intelv6.8_gccManualTerminalQuantum Espresso is a suite for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
siestav4.1.5v4.1.5_omp_mpiv4.1.5_omp_mpi_gcc11v4.1.5_omp_mpi_gcc11_testTerminalperforms electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
tinkerv6.3.01ManualTerminal
topmodv09Terminal
turbomolev6.0ManualTerminal
wannier90v2.0.0ManualTerminal
Functional analysis
Ingenuity-PathwayvlastManualWebModel, analyze, and understand the complex biological and chemical systems at the core of life science research with IPA
humann2v0.11.2Terminal
Gene expression
R-Bioconductorv3.5.1v3.6.0v4.0.2v4.1.0(default)v4.1.0_sinv4.1.2_visv4.1.2_vis_sinTerminalR statistical language
methpipev3.4.3ManualTerminal
mirdeep2v2Terminal
Genetic variations
TEtoolkitv160206Terminal
bayescanv2.1Terminal
breakdancerv1.1ManualTerminal
cambav012312Terminal
chimerascanv0.4.5aUse onlineTerminal
cnvkitv0.9.9Terminal
deepvariantv1.2.0Terminal
dellyv0.7.2v080115Terminal
encorev20121120Terminal
fastsimcoal2v2.5.2Use onlineTerminal
freebayesv1.3.6Terminal
gappav0.8.1Terminal
gatkv3.1v3.5v3.6.0v4.1.2.0v4.2.2.0(default)Terminal
kissplicev2.2.1ManualTerminal
lamplinkv1.11Terminal
mantav0.27.1v1.6.0ManualTerminal
metasvv0.5.2Use onlineTerminal
mrbayesv3.2.3Terminal
multisnvv15042015v27062015Use onlineTerminal
mutectv20141110Terminal
oncotatorv20150915ManualTerminal
phenolyzerv0.1.8Terminal
pilonv1.23Terminal
pindelv01102018ManualTerminal
plinkv1.05v1.07v1.09Use onlineTerminal
pradav1.2Terminal
repenrichv2_20170822v20150918Use onlineTerminalRepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
strelkav1.0.14Use onlineTerminal
trupv2015_10_13Use onlineTerminal
varcapv3.0ManualTerminal
varscanv2.3.6v2.4.3ManualTerminal
vcflibv20150325Terminal
Genome assembly
TGICLv2.1ManualTerminal
a5_miseqv20150522ManualTerminal
abyssv1.3.5v2.3.5Terminal
allpaths-lgv52488Terminal
amosv3.1.0Terminal
buscov1.1b1v2.0v3.0.2v5.2.2ManualTerminal
bwav0.5.9v0.7.5av0.7.12(default)Terminal
cabogv6.1v7.0(default)v8.3rc2ManualUse onlineTerminalWeb
canuv1.6v1.8v2.1.1v2.1.1_modifManualTerminal
cap3v101507v20130806ManualUse onlineTerminalWeb
casavav1.8.2Use onlineTerminal
celerav6.1v7.0(default)v8.3rc2ManualUse onlineTerminalWeb
copev1.1.3Terminal
cortexv1.0.5.21Terminal
discovarv52488Terminal
eulerv120408Terminal
falconv20160425Terminal
finisherscv2.0.29Terminal
gam-ngsv20131210Terminal
garmv0.7.3Terminal
gemBSv140921Use onlineTerminal
hifiasmv0.15.5v0.16.1ManualTerminal
kalignv2Terminal
kmergeniev1.7051Terminal
masurcav1.9.5v4.0.9Terminal
matsv3.0.9Use onlineTerminal
metassemblerv1.5Use onlineTerminal
miniav1.4683Terminal
minimap2v2.9Terminal
mirav3.2.0v4.0.2(default)v4.0rc4v4.9.6ManualUse onlineTerminalWeb
mspacv261120Terminal
mummerv3.22Terminal
newblerv2.8Terminal
oasesv0.2.08(default)v0.2.08_vel1.2.08TerminalDe novo transcriptome assembler for very short reads
pBWAv1.21009Use onlineTerminal
pb_assemblyv20210110TerminalPAcbio assembly
phusion2v20150108ManualTerminal
platanusv1.2.1v1.2.4Terminal
raconv1.5.0Terminal
ragtagv2.1.0Terminal
rayv1.7.0v2.3.1Terminal
roche454v2.8v2.9(default)Terminal
samstatv1.5.1(default)v1.09Terminal
scarpav0.22Terminal
scipiov1.4Terminal
sgav0.9.43v0.10.14(default)v0.10.14_10kTerminal
smrtanalysisv3.0.2Terminal
soap3dpv2.3.169Terminal
soapdenovov1.0.5vr223vr240(default)vr242ManualTerminal
soapdenovo_transv1.03TerminalA de novo transcriptome assembler designed specifically for RNA-Seq
spadesv3.5.0v3.7.1v3.10.1v3.14v3.15.4Terminal
sspacev3.0Terminal
stringtiev1.3.1cv1.3.3bTerminal
suttav1.0Terminal
tophatv1.4.1v2.0.4v2.0.8bv2.0.10v2.0.13v2.1.0Terminal
velvetv1.2.08v1.2.10ManualTerminal
vmatchv2.3.0ManualTerminal
wenganv0.2Terminal
Genomics tools
agentv2018Terminal
alignminerv110ManualUse onlineTerminalWeb
arcasHLAv20190903ManualTerminal
augustusv3.1v3.2.3v3.3Terminal
bactopiav20220127Terminal
bamtoolsv2.4.0Use onlineTerminal
bamutilv20190625Terminal
baypassv2.1Terminal
bcl2fastqv2.17.1.14v2.20(default)Terminal
bedopsv2.4.39v2.4.40Terminal
bedtoolsv2.20.1v2.26.0v2.28.0ManualTerminal
biocodev1.0Terminal
centrifugev1.0.3v1.0.4Terminal
circexplorer2v2.3.8Terminal
circrnav300421Use onlineTerminal
circtoolsv1.2.0Use onlineTerminal
clustAGEv0.8ManualTerminal
colonyv2.0.6.5Terminal
exome_depthv1.1.10Terminal
fastlmmv2.07Use onlineTerminal
fgbiov1.4.0Terminal
genometoolsv1.3.5v1.5.9Terminal
genotoolboxv20131009TerminalGenoToolBox is a collection of scripts used to manipulate genomic data
gffcomparev0.10.1ManualTerminal
glimmer-mgv0.3.1Terminal
glnexusv1.4.1Use onlineTerminal
gtdb-tkv1.7.0Terminal
hotspotv4.1.0Use onlineTerminal
krakenv2.1.2Terminal
kronav2.4Terminal
lfmmv1.4ManualTerminal
lofreqv2.1.3.1ManualTerminal
macs2v2.2.6Use onlineTerminal
map-rseqv1.2.1Terminal
mauvev2.3.1ManualTerminal
meganv5Terminal
memev5.1.1Terminal
metaeukv2020Terminal
metamosv1.2Terminal
miccav1.6.2v1.7.2ManualTerminal
migrate-nv3.6.11Use onlineTerminal
mmseqsv20220324Terminal
mrepsv2.5Terminal
multiqcv1.6v1.11v1.11_testManualTerminal
musclev2010Terminal
pacbiov5.1.0ManualTerminal
phylipv3.6ManualTerminal
picardv2.7.1(default)v2.20.2v2.22.1v20150416v20150908ManualTerminal
prankv270417Terminal
predicthaplov0.4Terminal
pyaniv0.2.10Terminal
pyphillinv20220118Terminal
qiimev1.9.1v2v2.2017.6v2.2018.2v2.2019.7v2.2021.4v2.2021.8v2.2021.11ManualTerminal
quiverv2.2.2ManualTerminal
qurev0.99971Terminal
radarv0.2.2Use onlineTerminal
repeatmaskerv4.1.0Terminal
repeatoirev20131009Terminal
rmblastv2.9.0Terminal
sambambav0.6.6v0.8.1Terminal
seqbusterv3.1Terminal
seqclusterv20150226Terminal
shorahv0.82Terminal
snippyv040419Terminal
sparccv050319Terminal
spinev150319ManualTerminal
starv2.4.0jv2.5.1bv2.5.3av2.7.6bv2.7.9aManualTerminal
star-fusionv1.0.0v1.10.0ManualTerminal
structurev2.3.4ManualUse onlineTerminal
tombov1.5Terminal
viquasv1.3Terminal
virusdetectv1.7ManualTerminal
wgdv1.2Use onlineTerminal
yampv0.9.5.3Terminal
Image processing
blenderv2.74Terminal
fijiv1.48iTerminal
fslv5.0.10Terminal
icyv1.4.3.5Terminal
imafish_mlv20160311Terminal
imagejv1.47Terminal
imagemagickv6.9.0-4Terminal
instant-ngpv170522Terminal
jasperv2.0.14Terminal
libtiffv4.0.6ManualTerminal
meshroomv2021.1Terminal
povv3.7Terminal
webpv0.4.0Terminal
wnd-charmv160713ManualTerminal
Libs
SuiteSparsev4.5.4_gcc_4.9.1Use onlineTerminalSuiteSparse is a suite of sparse matrix algorithms.
anacondav11-2020v39.4.9.2v2021.05versionTerminal
antlrv2.7.7Use onlineTerminal
armadillov6.700.6Terminal
beaglev2.1Terminal
berkely-dbv4.3.29v6.2.23Terminal
bisonv3.0.2Terminal
blisv3.1_aoccv3.1_gcc11ManualUse onlineTerminal
boostv1.36v1.44v1.55v1.64Terminal
byaccv1.9Terminal
bzip2v1.0.6Terminal
cudav4v5v6Terminal
eigenv3.2.8ManualTerminal
fftwv2.1.5_intel_mpiv3.3.3v3.3.3_intelv3.3.4v3.3.7_intel_mpiv3.3.10_ompi4_gcc11Terminalfast FFT compiled with intel compilers
filezillav3.29.0Terminal
flexv2.5.3Terminal
foam-extendv1.6v3.1v3.1_con1.6.5TerminalThe goal of this project is to open the OpenFOAM CFD toolbox to community contributed extensions.
freefemv3.51v3.51_mpiv3.54_mpiv3.55_mpiUse onlineTerminal
freetypev2.5.3Terminal
gapv4r5Terminal
geant4v10.5v10.7.2_gcc7.5.0ManualTerminaltoolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science
gem5v220422Terminal
glewv1.12.0Terminal
glibv2.0Terminal
glpk_oldv4.65Terminal
gmpv6.1.2v6.1.2_gcc_4.9.1Terminal
gperfv2.8.1Use onlineTerminal
gslv1.16v2.1v2.1_intelTerminal
h5pypv1.10.6.1a0Terminal
hdf5v1.8.12(default)v1.8.12_gccv1.8.12_gcc4v1.8.12_gcc4_mpiv1.8.12_intel_f_mpiv1.10.1_intelv1.10.5_gcc7.5.0_mpi1v1.10.5_mpichv1.10.5_mpich_gcc4v1.10.5_mpich_gcc7v1.12.0v1.12.0_gcc11v1.12.0_intelmpiv1.12.1_api16_gcc7.5.0_ompi3v1.12.1_api16_gcc7.5.0_ompi4v1.12.1_exav1.12.1_exa_cmakev1.12.1_gcc7.5.0_mpi1v1.12.1_gcc7.5.0_mpi3v1.12.1_gcc7.5.0_mpi3_nv1.12.1_gcc7.5.0_mpi4v1.12.1_gcc11v1.12.1_intel21TerminalHDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections
htslibv1.14Terminal
lapackv3.4.2(default)v3.5.0v3.6.0v3.8.0v3.9.1vmal_3.8.0TerminalLinear Algebra PACKage
lavavuv171130ManualTerminal
libatlasv3.10.1Terminal
libcurlv7.50.3Terminal
libdbv4.6Terminal
libgdalv2.1.3Terminal
libgit2v161220Terminal
libpcrev8.38v8.41Terminal
libpngv15Terminal
libxml2v2.7.8Use onlineTerminal
libyamlv0.1.4Terminal
libzmqv4.3.4Terminal
mavenv3.2.1v3.8.1Terminal
metisv5.1.0_gcc7.5.0v5.1.0_gcc11v5.1.0_intel2013v5.1.0_intel2021ManualTerminalSerial Graph Partitioning and Fill-reducing Matrix Ordering
motifv2.3.4Use onlineTerminal
mpfrv3.1.5Terminal
netCDFv1.12.1_pnet_intelv4.3.0v4.4.0_gccv4.4.2_gcc_fortranv4.4.2_gcc_fortran_mpiv4.7.0_intelv4.7.2_gcc4v4.7.2_gcc7v4.7.2_gcc9v4.8.0_gcc7v4.8.0_gcc7.5.0_mpiv4.8.0_gcc7.5.0_mpi3v4.8.0_gcc11v4.8.0_intelmpiv4.8.1_exav4.8.1_gcc7.5.0_mpi3v4.8.1_gcc7.5.0_ompi3_hdf51.12.1Api16v4.8.1_gcc7.5.0_ompi4_hdf51.12.1Api16v4.8.1_gcc11v4.8.1_intel214Use onlineTerminalNetwork Common Data Form (NetCDF) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
opencvv2Terminal
opendapv2.0Use onlineTerminal
openfoamv2.2.0v2.2.0_unpatchedv2.3.0v2.3.1v4_v1706Use onlineTerminalfluid dynamcis (CFD) software package
openfoam_extendv3.2_gccv3.2_gcc.bkpUse onlineTerminalfluid dynamcis (CFD) software package extended
opensslv1.0.2dv1.0.2f(default)v1.1.0eManualTerminal
petscv3.1.8v3.1.8mpichv3.7.7v3.8ManualTerminal
platypusv1.0.4Terminal
pnetCDFv1.12.1Use onlineTerminal
proj4v4.9.3Terminal
pytorchv0.4.1v1.11.0Terminal
qtv4.8.5v5.11.1v5.11.2ManualTerminal
rootv6.16v6.24.06_gcc7.5.0ManualTerminalA modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage
scalapackv2.0.2(default)v2.0.2_gccv2.0.2_intelv2.1.0_gcc7.5.0v2.1.0_gcc11v2.1.0_gcc11_nTerminalScalable Linear Algebra PACKage
sparsehashv2.0.2v2.0.3Terminal
swigv3.0.8Terminal
tauv2.30.1Terminal
tensorflowv0.9v1.12v1.15.5v2.0.0v2.3.0v2.3.0_pytorch_171v2.3.0_wandb_lastv2.4.0v2.5.0v2.5.0_libsv2.8.0Terminalopencv with tensorflow 2.2
wxv3.0.3Terminal
xdmfvgit_110416ManualTerminal
zlibv1.2.8v1.2.11Terminal
Molecular simulation
CHARMMv32b1ManualTerminal
amberv12v12mpiv16vcudaTerminal
ambertoolsv21v21mpiUse onlineTerminal
cpmdv3.13.2v3.15.3Terminal
gromacsv2022.2Terminal
lammpsv1feb14(default)Terminal
mdynamixv5.2.6Terminal
namdv2.8plumedv2.9v2.13b1vnb_2017_07_24Terminal
rosettav2017.26ManualTerminal
vaspv4.6v5.2v5.3.3(default)v5.3.3_vtstv5.3.5_vtstv5.4.1v5.4.1.05Feb16v5.4.1.05Feb16_testv5.4.1gnuTerminalVASP (Vienna Ab initio Simulation Package) is a program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics
Mpi
impiv4.1.0.024Terminal
mpichv3.3.1_gcc4v3.3.1_gcc7v3.3.1_gcc9ManualTerminal
openmpi_gccv1.10.6_gcc7.5.0v3.1.6_gcc7.5.0v4.1.1_exav4.1.1_gcc7.5.0(default)v4.1.1_gcc11.1.0v4.1.2_gcc7.5.0TerminalMPI library
openmpi_intelv1.6.1v4.1.1Terminal
Music tools
ffmpegv2013.05.15Terminal
flacv1.2.1Terminal
id3v0.15Terminal
lilypondv2.16.2Terminal
soxv14.4.1Terminal
timidityv2.14.0Terminal
uuid-runtimev2.17.2-9Terminaluuid generating tool
Oceanography
FVCOMv3.1.6v3.2.0Terminal
cdov2.0.1ManualTerminal
delft3dv7545Terminal
ecmwfv2.17.0ManualTerminal
hermesv1.0.2v2.1.2Terminal
ncov5.0.3Terminal
qgisv3.14.16Use onlineTerminal
shyfemv7.5.71v250521ManualUse onlineTerminal
Optimizers
amplv20200501v20200501_user_licv20210425TerminalAMPL is an algebraic modeling system used for optimization.
coin-orv1.7.4Terminal
gurobiv9.0.1v9.5.1ManualTerminal
ipoptv3.12.8Terminal
Physics
CST_Studiov2022Terminal
MohidWaterv160517ManualTerminal
WRFv3.9.1.1v3.9.1.1_modifv4.2.2_2021v4.2.2_gcc11ManualTerminal
ansysv14v18.2v19.1v19.2v20.2v21.1v21.1_testv21.2v22.1Use onlineTerminal
basiliskv130319Terminal
cern_rootv6.08.00ManualUse onlineTerminal
channelflowv1.5.1ManualTerminal
comsolv4.3bv4.4v5.2v5.6Use onlineTerminal
nclv6.6.2ManualTerminal
oxcalv4.3ManualTerminal
pandapowerv2.6.0v2.6.0_nTerminal
parallel_bilbyv1.1.3TerminalBayesian inference library, primarily for inference of compact binary coalescence events in interferometric data
udunitsv2.2.19Use onlineTerminal
Programming languages
Rv3.5.1v3.6.0v4.0.2v4.1.0(default)v4.1.0_sinv4.1.2_visv4.1.2_vis_sinTerminal
bioperlv1.4v1.6.1(default)v1.7.7Terminal
chapelv1.6.0v1.6.181212v1.10.0Terminal
cmakev2.8.8v3.5.1v3.13.1v3.21.4Terminal
cplexv12.6.3cmv20.1.0v20.1.0_21v20.1.0_21nTerminal
cvxoptv1.2.3ManualTerminal
degeneshunterv0.98v0.99.13Terminalcomprehensive protocol for the analysis of transcriptional data
gamsv24.2.2ManualTerminal
gccv4.4.7v4.5.4v4.6.2v4.9.1v4.9.4v5.5.0v7.2.0v9.2.0v11.1.0Terminal
glpkv4.65Terminal
gov1.11.1v1.14(default)Terminal
gprof2dotv20191130ManualTerminal
intelv2013.1.117v2021.2v2021.4(default)v2021.4_sinmpiTerminal
javav1.6.0_18vjdk-7u40vjdk-8u121vjdk-17.0.1vjre-7u21vjre-7u40vjre-8u60vjre-8u211vjre-8u301(default)Terminal
llvmv3.9.1Terminal
mathematicav11.2v12.3Terminal
matlabvR2007bvR2011bvR2012bvR2013bvR2014avR2014bvR2015b(default)vR2015b_jvmvR2015b_runtimevR2017bvR2019bvR2019b_runtimeTerminalMatlab numeric calculus programming and simulations
nodejsv6.11.3Terminal
nvhpcv20.9v20.9_nompiTerminal
octavev4.0.1v5.1.0Terminal
perlv5.8.9v5.14.2v5.28.2Terminal
pgiv13.6Terminal
pythonv2.7.18v3.8.8v3.8.10Terminal
rubyv1.9.3p327(default)v1.9.3p327_with_Rv2.2.2p95v2.3.4v2.3.8v2.4.1v2.7.2TerminalRuby programming language
sagev8.0ManualTerminal
singularv4.2.1Terminal
uprofv3.4.502Terminal
Quantum
cirqv0.11.0Use onlineTerminal
dwavev3.3.0Use onlineTerminal
qcgpuv0.1.1Use onlineTerminal
qiskitv0.8.2Terminal
Read mapping
bismarkv0.19.0v0.23.1ManualTerminal
bowtiev1.0v2.1.0v2.2.4v2.2.9v2.4.4v1.1.2v1_0.12.8v2_2.0.0-beta7TerminalRead mapping utility
gem3v3.6Terminal
gmapv7Terminal
gsnapv7Terminal
hisatv2.0.1bv2.0.5v2.1.0v2.2.1ManualTerminal
mafftv7.475Use onlineTerminal
stampyv1.0.32ManualTerminal
Sequences matching
blastv2.2.20Terminal
blast_plusv2.2.26+v2.2.27+v2.2.27+_stdv2.2.28+v2.2.29+v2.2.29_pipesv2.2.30+(default)v2.10.1+v2.12.0+Terminalfind matches between input and databases
blatv34Terminal
clustalv1.2.0_omegav2.1Terminal
diamondv0.9.22v2.0.13Terminal
exoneratev2.2.0Terminal
gpu_blastv2.2.28+Terminal
hmmerv3.1b1v3.1b2v3.3.2Terminal
platypusvcv0.8.1Terminal
scbi_distributed_blastv0.0.5TerminalDistributed blast+ using scbi_mapreduce
Sequences preprocessing
angsdv140515Use onlineTerminal
bbmapv36.11v37.68v38.50bTerminal
cdhitv4.5.4v4.8.1Terminal
cutadaptv3.4Terminal
deeptoolsv3.5.1Terminal
fastq-mcfv1.1.2Terminal
fastqcv0.10.1v0.11.4Use onlineTerminal
full_lengther_nextv0.0.8v0.5.6v1.0.1vlast(default)ManualUse onlineTerminalWebFull length sequences
hydrav0.5.3Terminal
ngs_qcv2.3Terminal
phredv0.020425.cTerminal
seqkitv0.10.1v2.2.0ManualTerminal
seqtrimbbv2.1.3v2.1.8Terminal
seqtrimnextv2.0.60v2.0.68(default)vlastManualUse onlineTerminalWeb
trimmomaticv0.32v0.35(default)ManualTerminal
Tests
Rv4.1.0_oldv4.1.0_visTerminal
REDItoolsv2.0Terminal
artaiosv2.1Terminal
bbmapv38.92Terminal
biobambamv2.0.180Terminal
bwav0.7.8Terminal
bwa_memv2.2.1Terminal
checkmv1.1.3Terminal
enveomicsv1.3.4Terminal
fastpv0.22.0ManualTerminal
fastqcv0.11.9Use onlineTerminal
fftwv3.3.9v3.3.9_openmpi3Terminalfast FFT compiled with intel compilers
gmapv2021_augTerminal
gnuplotv5.4.2Terminal
gsnapv2021_augTerminal
hyprev2.11.2_mpi1_gcc7.5.0v2.11.2_mpi4_gcc7.5.0v2.22.0v2.22.0_mpi1_gcc7.5.0v2.22.0_ompi3_gcc7.5.0TerminalHYPRE is a library of high performance preconditioners and solvers featuring multigrid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
idbav1.1.3Terminal
iqtreev1.6.12Terminal
juliav1.7.2Terminal
lapackv3.2.1v3.10.0_gcc7.5.0v3.10.0_gcc11TerminalLinear Algebra PACKage
matlabvR2020bTerminalMatlab numeric calculus programming and simulations
maxbinv2.2.7Terminal
megahitv1.2.9Terminal
mesmerv5.2Terminal
nanofiltv2.8Terminal
nanoplotv1.2Terminal
nanostatv1.5Terminal
picardv2.18.9ManualTerminal
plinkv1.90_betaUse onlineTerminal
prodigalv2.6.3_gcc11TerminalProdigal provides fast, accurate protein-coding gene predictions in GFF3, Genbank, or Sequin table format. It does not need to be provided with any training data, and instead automatically learns the properties of the genome from the sequence itself, including RBS motif usage, start codon usage, and coding statistics. Handles gaps and partial genes.
quastv5.0.2_gcc11Terminal
satsuma2v2020Terminal
squeezemetav1.3Terminal
tabixv0.2.6Terminal
trimmomaticv0.36v0.39ManualTerminal
Transcriptome assembly
cufflinksv2.0.2v2.1.1v2.2.1Terminal
pricev0.17.2Terminal
rsemv1.1.21v1.2.7v1.2.12Terminal
trinityv2.10.0v2.10.0.bkpvr2012.10.05vr2013.08.14vr2013.11.10vr2014.04.13p1vr2016.03.17_v2.2.0vr2017.02.05_v2.4.0TerminalTranscriptome assembly software
Transcriptomics tools
HTSeqv0.13.5v1.99.2ManualTerminal
UClncRv1.0.1v1.1.1ManualTerminal
alphafoldv20210907Terminal
annocriptv0.2Terminal
capmirseqv20140618Terminal
circomparav20190910Terminal
imrepv20190910Terminal
kallistov0.43.0Terminal
methyldackelv0.6.1Terminal
miarmav1.5Terminal
mireaderv2Terminal
nanocountv0.2.5Terminal
neofusev1.1.1ManualTerminal
pitav07Terminal
salmonv1.2.1v1.4.0ManualTerminal
squidv1.3Terminal
starchipv20190910Terminal
subreadv2.0.0v2.0.3ManualTerminal
tetoolsv2.0.3v020218ManualTerminal
transdecoderv20140704TerminalTransDecoder identifies 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
viennaRnav2.2.10Terminal
Utils
apsv0.1v0.2v0.9(default)v1.0Terminal
artv04022013Terminal
asperav3.9.6Terminal
autoflowv0.8.7vdevvlast(default)voldTerminal
bcftoolsv1.4ManualTerminal
chromonomerv1.10Terminal
circosv0.67-7Terminal
dimemasv5.4.2Terminal
dna2pepv1.1Terminal
dotv2.49.2Terminal
embossv6.6.0v6.6.0_nTerminal
evefv1.0v1.1v2.0Terminal
extraev3.8.0Terminal
fqbinv0.9Terminal
ghostscriptv8.64Terminal
git_lfsv20190923ManualTerminal
gnuplotv4.4.2v4.6.5Terminal
graphvizv2.49.2Terminal
inelasticav1.3.7Terminal
latexv3.14Terminal
lep_anchorv20200310Terminal
lep_map3v20200115Terminal
libgdv2.1.1Terminal
minicondav3Terminal
mysqlv5.6.23Terminal
ncbi_cpp_toolkitv12.0.0v21.0.0TerminalNCBI toolkit for C++
nextflowv20.10Terminal
pandocv2.2.1v2.11v2.17.0.1Terminal
parallelv20150322Terminal
paraverv4.8.2Terminal
parse_nanov01Terminal
picrustv1.1.3v1.1.4v2.0.3v2.5Terminal
portraitv1.1Terminal
prosplignv1.0.0Terminal
qualimapv2.2v2.2.1Terminal
rdkitv20140902v20150301Terminal
resv1.0Terminal
resmapv1.1.4Terminal
rtg-corev3.6Terminal
sam2countsv20131126v20131126_oldTerminalConvert SAM mapping results to reference sequence counts
samtoolsv0.1.16v0.1.19v1.3v1.3.1v1.12v1.13(default)ManualTerminal
singularityv3.5.3v3.7.2Terminal
solexaqav3.1.4Terminal
sparkv3.0.0_h3.2Terminal
splignv1.39.8Terminal
sra_toolkitv2.8.1v2.10.5Use onlineTerminal
vcev6.0.2Terminal
vcftoolsv0.1.11v20160205Terminal
vtcv0.9.2Terminal
wombatv20140828v20171103v20200225(default)Terminal
Visualization
VMDv1.9.1Use onlineTerminal
amirav550Terminal
gdalv2.1.1ManualTerminal
geosv3.7.0ManualTerminal
gracev5.1.23v5.1.25Use onlineTerminal
ncviewv2.1.7v2.1.7_newManualTerminal
paraviewv5.6.0Terminal
pymolv1.7.4Terminal
relionv1.3v1.4v2_beta_161031v2_beta_161031_guiManualTerminalRelion employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
seabornv0.9.0ManualTerminal
vis5dv1.3.0bTerminal
visitv3.2.2ManualUse onlineTerminal
xcrysdenv1.5.32Terminal
xmakemolv5.16Use onlineTerminal
xmippv3.1Use onlineTerminal

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