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.
Annotation
annotsvv3.1Terminal
brakerv2.1.5Terminal
dfast_corev1.2.18Terminal
dramv1.4.6Terminal
eggnog-mapperv2.1.6Terminal
genotev0.5b1Terminal
interproscanv5.44.79v5.54.87TerminalAnotación de proteinas
lionv171220Terminal
orthofinderv2.5.2Terminal
prokkav1.12v1.14.5Terminal
roaryv3.13.0Terminal
scbi_variantsvcurrentTerminalhtml generation
sma3v2v2.1v2.1_perlv2.2Terminal
snpeffv4.2v4.3v4.4v5eTerminal
unifamv1.0.0Terminal
vepv95.2Terminal
Chemistry
ABCClusterv2.1Terminal
MZminev3.9.0Terminal
artaiosv2.1Terminal
columbusv7.2Terminal
crystalv2.0.1mpiv14_1_0_2v14_1_0_2mpiv14_1_0_3v14_1_0_3mpiv17_intelv17_intel_2023v17_ompiManualTerminala tool for quantum simulation in solid state chemistry
daltonv2018_git_mpiv2020_gcc11_mpiv2020_gcc11_mpi_new2023Use 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
gatev8.2v9.1_gcc7.5.0v9.2_gcc12Terminal
molcasv7.8v7.8_ompv8.0v8.0gpuv8.01(default)v8.2v8.2_gfortv8.2_modifv8.2_mpi_modifv8.4v8.4_2022v8.4_amd_intelv8.4_nv8.4betav8.4beta_intelv8.6vopen_22.6_gcc12.2.0vopen_22.6_mklvopen_22.10_mkl_intel22ManualTerminalMolcas allow an accurate ab initio treatment of very general electronic structure problems for molecular systems
moldenv5.1v7.1Terminal
quantumespressov5.1v6.5_intelv6.8_gccv7.1_aocc_OMPv7.1_gpuv7.2_mpi4_gcc12ManualTerminalQuantum 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_testv4.1.5_omp_mpi_withTBtransManualTerminalperforms electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
siriusv5.8.1v5.8.5Terminal
topmodv09Terminal
Functional analysis
Ingenuity-PathwayvlastManualWebModel, analyze, and understand the complex biological and chemical systems at the core of life science research with IPA
home_biov0922Terminal
humann2v0.11.2Terminal
Gene expression
R-Bioconductorv3.2.5v3.5.1v3.6.0v4.0.2v4.1.0v4.1.0_oldv4.1.0_sinv4.1.0_visv4.1.2_visv4.1.2_vis_sinv4.2.1_vis(default)v4.2.2_visv4.3.1_gdalTerminalR statistical language
controlfreecv11.6Terminal
mirdeep2v2.0.1.3_2023v2.0.1.3_v2_2023TerminalDiscovers active known or novel miRNAs from deep sequencing data.
srnatoolboxv0.6Terminal
Genetic variations
TEtoolkitv160206Terminal
bayescanv2.1Terminal
cambav012312Terminal
cnvkitv0.9.9v0.9.10Terminal
deepvariantv1.2.0Terminal
dellyv0.7.2v080115Terminal
dictysv0.1.0Terminal
encorev20121120Terminal
freebayesv1.3.6Terminal
gappav0.8.1Terminal
gatkv3.1v3.5v3.6.0v4.1.2.0v4.2.2.0(default)v4.4.0.0Terminal
lamplinkv1.11Terminal
mrbayesv3.2.3Terminal
mutectv20141110Terminal
phenolyzerv0.1.8Terminal
pilonv1.23Terminal
plinkv1.05v1.07v1.09v1.90_betaTerminal
pradav1.2Terminal
repenrichv2_20170822v20150918Use onlineTerminalRepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
vcflibv20150325Terminal
Genome assembly
abyssv1.3.5v2.3.5Terminal
allpaths-lgv52488Terminal
amosv3.1.0Terminal
bwav0.5.9v0.7.5av0.7.8v0.7.12(default)v0.7.17Terminal
copev1.1.3v1.2.5_gccTerminal
cortexv1.0.5.21Terminal
discovarv52488Terminal
eulerv120408Terminal
falconv20160425Terminal
finisherscv2.0.29Terminal
gam-ngsv20131210Terminal
garmv0.7.3Terminal
homerv4.11.1Terminal
kalignv2Terminal
kmergeniev1.7051Terminal
masurcav1.9.5v3.2.4v4.0.9Terminal
megahitv1.2.9Terminal
miniav1.4683Terminal
minimap2v2.9v2.24Terminal
mspacv261120Terminal
mummerv3.22v3.23v4rc1Terminal
newblerv2.8Terminal
nextDenovov2.5.2Terminal
oasesv0.2.08(default)v0.2.08_vel1.2.08TerminalDe novo transcriptome assembler for very short reads
operamsv0.8.3Terminal
pb_assemblyv20210110TerminalPAcbio assembly
platanusv1.2.1v1.2.4Terminal
quastv5.0.2_gcc11v5.2.0Terminal
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
soapdenovo_transv1.03TerminalA de novo transcriptome assembler designed specifically for RNA-Seq
spadesv3.5.0v3.7.1v3.10.1v3.14v3.15.4Terminal
sspacev3.0Terminal
stringtiev1.3.1cv1.3.3bv2.2.1Terminal
suttav1.0Terminal
tophatv1.4.1v2.0.4v2.0.8bv2.0.10v2.0.13v2.1.0Terminal
wenganv0.2Terminal
Genomics tools
REDItoolsv2.0Terminal
SNAPvoct2022Terminal
agatv0.8.1Terminal
agentv2018Terminal
augustusv3.1v3.2.3v3.3Terminal
b2btoolsv3.0.6Terminal
bactopiav2.0.1v2.2.0Terminal
bamutilv20190625Terminal
barrnapv0.9Terminal
baypassv2.1Terminal
bcl2fastqv2.17.1.14v2.20(default)v2.20_gcc7Terminal
bedopsv2.4.39v2.4.40Terminal
biobambamv2.0.180Terminal
biocodev1.0Terminal
brackenv2.8Terminal
cell2locationv0.1.3v0.1.3_gpuTerminalComprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
centrifugev1.0.3v1.0.4Terminal
checkmv1.1.3Terminal
circexplorer2v2.3.8Terminal
colonyv2.0.6.5Terminal
dada2v1.26.0Terminal
eigensoftv8.0.0Terminal
enveomicsv1.3.4Terminal
epangv0.3.8Terminal
exome_depthv1.1.10Terminal
expansionhunterv5.0.0TerminalThere are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat
fgbiov1.4.0Terminal
fldpnnv12_2021Terminal
genomescopev2.0vpaperTerminal
genometoolsv1.3.5v1.5.9Terminal
genotoolboxv20131009TerminalGenoToolBox is a collection of scripts used to manipulate genomic data
gffreadv0.12.7Terminal
glimmer-mgv0.3.1Terminal
grenedalfv0.3.0Terminal
gtdb-tkv1.7.0Terminal
haplomerge2v20180603TerminalHaploMerger2 is an automated pipeline designed to facilitate the construction of a highly polymorphic diploid genome assembly.
idbav1.1.3Terminal
infernalv1.1.4Terminal
iqtreev1.6.12Terminal
jeSuitv2.0.RCTerminal
jellyfishv2.3.0Terminal
krakenv2.1.2v2.1.3Terminal
kraken-biomv1.0.1Terminal
krakentoolsv1.2Terminal
kronav2.4Terminal
map-rseqv1.2.1Terminal
maxbinv2.2.7Terminal
meganv5Terminal
memev5.1.1v5.5.0Terminal
metaeukv2020Terminal
metamosv1.2Terminal
metawrapv1.3.0_mgTerminal
mmseqsv20220324Terminal
mmseqs2v14.7Terminal
mobidb_litev3.8.4Terminal
mrepsv2.5Terminal
multiqcv1.6v1.11v1.11_testv1.13aTerminal
musclev2010Terminal
nanofiltv2.8Terminal
nanoplotv1.2Terminal
nanostatv1.5Terminal
paparav2.5Terminal
phantompeakqualtoolsv1.2.2TerminalThis package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
phylophlanv3.0.3Terminal
picnicv10_2023Terminal
popoolation2v1Terminal
prankv270417Terminal
predicthaplov0.4Terminal
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.
purge_haplotigsv1.1.2TerminalA simple pipeline for reassigning primary contigs that should be labelled as haplotigs.
pyaniv0.2.10v0.2.12Terminal
pyphillinv20220118Terminal
qapv1.2.1Terminal
qiimev1.9.1Terminal
qiime2v2017.6v2018.2v2018.2_oriv2019.7v2021.4v2021.8v2021.11v2023.2v2023.5.0v2023.5.0_withRESCRIPtv2023.5.1ManualTerminalpipeline for performing microbiome analysis from raw DNA sequencing data
qurev0.99971Terminal
rasflowv2020Terminal
raxmlv8.2.12Terminal
raxml-ngv1.1.0Terminal
repeatmaskerv4.1.0v4.1.4v4.1.5Terminal
repeatmodelerv2.0.4v2.0.4_newTerminalRepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.
repeatoirev20131009Terminal
rmblastv2.9.0v2.14.0Terminal
sambambav0.6.6v0.8.1v1.0.1Terminal
samblasterv0.1.26Terminal
seqbusterv3.1Terminal
seqclusterv20150226Terminal
sequeltoolsv1.3.4Terminal
shorahv0.82Terminal
snape-pooledv2013Terminal
snippyv040419Terminal
snptestv2.5.6Terminal
sortmernav4.3.6Terminal
sparccv050319Terminal
squeezemetav1.3v1.6.1post1v1.6.2port3v1.6.3TerminalSqueezemeta is a fully automated metagenomics pipeline, from reads to bins
syriv1.6.3Terminal
tRNAscanv2.0.12Terminal
tombov1.5Terminal
trfv4.09.1v4.09.1_gcc12Terminal
trimalv1.4.1Terminal
viquasv1.3Terminal
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
meshroomv2021.1Terminal
povv3.7Terminal
webpv0.4.0Terminal
Libs
anacondav11-2020v39.4.9.2v2021.05v2022.10versionTerminal
armadillov6.700.6v7.960.2Terminal
beaglev2.1Terminal
berkely-dbv4.3.29v6.2.23Terminal
bisonv3.0.2Terminal
boostv1.36v1.44v1.55v1.64v1.64.0v1.80Terminal
byaccv1.9Terminal
bzip2v1.0.6Terminal
cudav4v5v6Terminal
fftwv2.1.5_intel_mpiv3.3.3v3.3.3_intelv3.3.4v3.3.7_intel_mpiv3.3.7_mpi4_gcc7v3.3.9v3.3.9_openmpi3v3.3.10_intel22v3.3.10_intel_mpi4v3.3.10_ompi4_gcc7.5v3.3.10_ompi4_gcc9.5v3.3.10_ompi4_gcc11v3.3.10_ompi4_gcc13Terminalfast 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.
freetypev2.5.3Terminal
gapv4.12.1v4r5Terminal
geant4v10.5v10.5_gcc7.2_2023v10.5_gcc12_2023v10.7.2_gcc7.5.0v11.1.2_gcc12ManualTerminaltoolkit 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
globalarraysv5.8.1v5.8.2_intel22TerminalGlobal Arrays is a portable Non-Uniform Memory Access (NUMA) shared-memory programming environment for distributed and shared memory computers
glpk_oldv4.65Terminal
gmpv6.1.2v6.1.2_gcc_4.9.1Terminal
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_intel21v1.12.2_intel22v1.12.2_intel_mpi4v1.12.2_intel_mpichv1.14.2_gcc7.5.0v1.14.2_gcc7.5.0_mpi4.1.2TerminalHDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections
htslibv1.14v1.16Terminal
lapackv3.2.1v3.4.2(default)v3.5.0v3.6.0v3.8.0v3.9.1v3.10.0_gcc7.5.0v3.10.0_gcc11v3.11.0_gcc12v3.11.0_gcc13vmal_3.8.0TerminalLinear Algebra PACKage
libatlasv3.10.1Terminal
libcurlv7.50.3Terminal
libdbv4.6Terminal
libgdalv2.1.3Terminal
libgit2v161220Terminal
libpcrev8.38v8.41Terminal
libpngv15Terminal
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_intel2021v5.1.0_mpi4.1.4_gcc12ManualTerminalSerial Graph Partitioning and Fill-reducing Matrix Ordering
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_intel214v4.8.1_intel214_cv4.8.1_intel214_c_fortranv4.8.1_intel214_fortranv4.8.1_intel223_cv4.9.0_c_fortran_gcc12.2.0_mpi4.1.4v4.9.0_c_fortran_mpich_4v4.9.2_c_fortran_gcc7.5.0v4.9.2_c_fortran_intel214_mpi4.1.1v4.9.2_c_fortran_intel214_mpiiccv4.9.2_c_fortran_intel214_mpiicc_newUse 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
openblasv0.3.21v0.3.21_nTerminal
opencvv2Terminal
openfoamv2.2.0v2.2.0_unpatchedv2.3.0_swak4Foam_2023v2.3.1v4_v1706v2212v2306Use onlineTerminalfluid dynamcis (CFD) software package
platypusv1.0.4Terminal
pytorchv0.4.1v1.11.0v2.0.0a1767026Terminalpytorch 2.0.0a0+1767026 with libraries
rootv6.16v6.24.06_gcc7.2_no_geant_2023v6.24.06_gcc7.5.0v6.24.06_gcc7.5_no_geant_2023v6.26.10_gcc12v6.26.10_gcc12_no_Geant_2023ManualTerminalA 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_nv2.2.0_gcc12TerminalScalable 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_libsv2.8.0v2.9.1v2.10.0v2.11.0v2.13.0Terminalopencv with tensorflow 2.2
wxv3.0.3Terminal
zlibv1.2.8v1.2.11Terminal
Molecular simulation
amberv12v12mpiv16vcudaTerminal
cpmdv3.13.2v3.15.3v4.3Terminal
gromacsv2022.2v2022.3_impiv2023.3v2023.3_gpuv2023.3_mklTerminal
lammpsv1feb14(default)Terminal
mdynamixv5.2.6Terminal
vaspv4.6v5.2v5.3.3(default)v5.3.3_vtstv5.3.5_vtstv5.4.1v5.4.1.05Feb16v5.4.1gnuv5.4.4_2023v6.3.0-amd_2023Terminal
Mpi
impiv4.1.0.024Terminal
openmpi_aoccv4.1.1Terminal
openmpi_gccv1.10.6_gcc7.5.0v3.1.6_gcc7.5.0v3.1.6_gcc12.2.0_ucxv4.1.1_exav4.1.1_gcc7.5.0(default)v4.1.1_gcc11.1.0v4.1.2_gcc7.5.0v4.1.4_gcc9.5.0_cudav4.1.4_gcc12.2.0_ucxv4.1.5_gcc9.5.0_cudav4.1.5_gcc13.2.0TerminalMPI library
openmpi_intelv1.6.1v4.1.1Terminal
ucxv1.13.1v1.14.1Terminal
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
delft3dv7545Terminal
hermesv1.0.2v2.1.2Terminal
ncov5.0.3v5.1.6Terminal
Optimizers
amplv20200501v20200501_user_licv20210425v20220424v20230423TerminalAMPL is an algebraic modeling system used for optimization.
coin-orv1.7.4Terminal
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.
ipoptv3.12.8Terminal
Physics
CST_Studiov2022Terminal
WRFv3.9.1.1v3.9.1.1_intel_2023v3.9.1.1_modifv4.2.2_2021v4.2.2_gcc11v4.4.2_gcc12_mpiv4.4.2_intel_mpiManualTerminalWeather Research and Forecasting Model
asev3.22.1Terminal
bagelv1.2.2Terminal
basiliskv130319Terminal
einstein_toolkitv2022ManualUse onlineTerminalThe Einstein Toolkit is a community-driven software platform of core computational tools to advance and support research in relativistic astrophysics and gravitational physics.
meepv1.25Terminal
mesmerv5.2Terminal
pandapowerv2.6.0v2.6.0_nTerminal
parallel_bilbyv1.1.3TerminalBayesian inference library, primarily for inference of compact binary coalescence events in interferometric data
udunitsv2.2.19v2.2.19_gcc7v2.2.19_intel22Use onlineTerminalThe UDUNITS package supports units of physical quantities, contains an extensive unit database and allows investigating units and converting values
Programming languages
Rv3.2.5v3.5.1v3.6.0v4.0.2v4.1.0v4.1.0_oldv4.1.0_sinv4.1.0_visv4.1.2_visv4.1.2_vis_sinv4.2.1_vis(default)v4.2.2_visv4.3.1_gdalTerminal
aoccv3.2.0Terminal
aoclv4.0_with_aocc_4.0v4.0_with_gcc_11.2Terminal
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
degeneshunterv0.98v0.99.13Terminalcomprehensive protocol for the analysis of transcriptional data
gccv4.4.7v4.5.4v4.6.2v4.9.1v4.9.4v5.5.0v7.2.0v9.2.0v9.5.0v11.1.0v12.2.0v13.1.0v13.2.0Terminal
glpkv4.65Terminal
gov1.11.1v1.14(default)Terminal
intelv2013.1.117v2021.2v2021.4(default)v2021.4_sinmpiv2022.3v2023.1Terminal
javav1.6.0_18vjdk-7u40vjdk-8u121vjdk-17.0.1vjre-7u21vjre-7u40vjre-8u60vjre-8u211vjre-8u301(default)Terminal
juliav1.7.2Terminal
llvmv3.9.1Terminal
mathematicav11.2v12.3Terminal
matlabvR2007bvR2011bvR2012bvR2013bvR2014avR2014bvR2015b(default)vR2015b_jvmvR2015b_runtimevR2017bvR2019bvR2019b_runtimevR2020bvR2022bvR2022b_mccvR2022b_pythonvR2023bTerminalMatlab numeric calculus programming and simulations
nasmv2.15.05Terminal
nodejsv6.11.3Terminal
nvhpcv20.9v20.9_nompiTerminal
octavev4.0.1v5.1.0Terminal
perlv5.8.9v5.14.2v5.28.2v5.36.0Terminal
pgiv13.6Terminal
pythonv2.7.18v3.8.8v3.8.10v3.9.1v3.9.13v3.11.4Terminal
rubyv1.9.3p327(default)v1.9.3p327_with_Rv2.2.2p95v2.3.4v2.3.8v2.4.1v2.7.2TerminalRuby programming language
rustv1.67.1Terminal
singularv4.2.1Terminal
uprofv3.4.502Terminal
Quantum
cirqv0.11.0v1.1.0_with_qiskit_qibo_dwaveTerminalA python framework for creating, editing, and invoking Noisy Intermediate Scale Quantum (NISQ) circuits. The module has also Qiskit 0.43.0 with GPU and MPI suport, Dwave (Ocean) 6.3.0, Qibo 0.1.13
dwavev3.3.0v6.3.0_with_qiskit_qibo_cirqTerminalQiskit is an open-source SDK for working with quantum computers at the level of pulses, circuits, and application modules. This version is compiled with GPU and MPI support. The module has also Cirq 1.1.0, Dwave (Ocean) 6.3.0, Qibo 0.1.13.
qibov0.1.12v0.1.13_with_qiskit_cirq_dwaveTerminalQibo is an open-source full stack API for quantum simulation and quantum hardware control. The module has also Qiskit 0.43.0 compiled with GPU and MPI support, Cirq 1.1.0, Dwave (Ocean) 6.3.0
qiskitv0.8.2v0.37.1v0.37.2_gpuv0.38.0v0.39.0_mpiv0.39.1_gpuv0.43.0_gpu_mpiv0.43.0_with_qibo_cirq_dwaveTerminalQiskit is an open-source SDK for working with quantum computers at the level of pulses, circuits, and application modules. This version is compiled with GPU and MPI support.
Read mapping
bowtiev1.0v1.3.1v2.1.0v2.2.4v2.2.9v2.4.4v2.5.1v1.1.2v1_0.12.8v2_2.0.0-beta7Sample scriptTerminalRead mapping utility
gem3v3.6Terminal
gmapv2021_augv7Terminal
gsnapv2021_augv7Terminal
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+v2.13.0+Sample scriptTerminalfind matches between input and databases
blatv34Terminal
bwa_memv2.2.1Terminal
clustalv1.2.0_omegav2.1Terminal
diamondv0.9.22v2.0.13v2.0.15v2.1.8Terminal
exoneratev2.2.0Terminal
gpu_blastv2.2.28+Terminal
hmmerv3.1b1v3.1b2v3.2.1_gcc12v3.3.2Terminal
lastzv1.04.22Terminal
platypusvcv0.8.1Terminal
scbi_distributed_blastv0.0.5TerminalDistributed blast+ using scbi_mapreduce
Sequences preprocessing
bbmapv36.11v37.68v38.50bv38.92Terminal
cdhitv4.5.4v4.8.1Terminal
cellrangerv7.0.0Terminal
cellranger-arcv2.0.1TerminalCell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage
cutadaptv3.4v4.4Terminal
deeptoolsv3.5.1Terminal
fastq-mcfv1.1.2Terminal
fastqcv0.10.1v0.11.4v0.11.9Terminal
hydrav0.5.3Terminal
ngs_qcv2.3Terminal
phredv0.020425.cTerminal
seqtrimbbv2.1.3v2.1.8Terminal
Transcriptome assembly
cufflinksv2.0.2v2.1.1v2.2.1Terminal
pricev0.17.2Terminal
rsemv1.1.21v1.2.7v1.2.12v1.3.3Terminal
trinityv2.10.0v2.10.0.bkpv2.13.2v2.14.0v2.15.1vr2012.10.05vr2013.08.14vr2013.11.10vr2014.04.13p1vr2016.03.17_v2.2.0vr2017.02.05_v2.4.0TerminalTranscriptome assembly software
Transcriptomics tools
alphafoldv2.3.1Terminal
annocriptv0.2Terminal
capmirseqv20140618Terminal
circomparav20190910Terminal
imrepv20190910Terminal
kallistov0.43.0Terminal
methyldackelv0.6.1Terminal
miarmav1.5Terminal
mireaderv2Terminal
msisensorprov1.2.0Terminal
nanocountv0.2.5Terminal
pitav07Terminal
squidv1.3Terminal
starchipv20190910Terminal
tidditv3.3.2Terminal
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
bamaddrgv9baba65Terminal
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
gnuplotv4.4.2v4.6.5v5.4.2Terminal
graphvizv2.49.2Terminal
inelasticav1.3.7Terminal
latexv3.14v3.14_singTerminal
lep_anchorv20200310Terminal
lep_map3v20200115Terminal
libgdv2.1.1Terminal
memtesterv4.6.0Terminal
minicondav3v3_py10Terminal
mysqlv5.6.23Terminal
ncbi_cpp_toolkitv12.0.0v21.0.0TerminalNCBI toolkit for C++
nextflowv20.10v23.10Terminal
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
pydrive2v0.14.0Terminal
qualimapv2.2v2.2.1Terminal
rdkitv20140902v20150301Terminal
resv1.0Terminal
resmapv1.1.4Terminal
rtg-corev3.6Terminal
sam2countsv20131126v20131126_oldTerminalConvert SAM mapping results to reference sequence counts
singularityv3.5.3v3.7.2Terminal
solexaqav3.1.4Terminal
sparkv3.0.0_h3.2Terminal
splignv1.39.8Terminal
statav17Terminal
sysbenchv1.0.20Terminal
tabixv0.2.6Terminal
vcftoolsv0.1.11v20160205Terminal
vtcv0.9.2Terminal
Visualization
amirav550Terminal
fltkv1.4.0Terminal
paraviewv5.6.0v5.11.2Terminal
pymolv1.7.4Terminal
relionv1.3v1.4v2_beta_161031v2_beta_161031_guiv4.0v4.0_guiUse onlineTerminalRelion employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
vis5dv1.3.0bTerminal
xcrysdenv1.5.32Terminal