Installed Software
CRC uses the lmod environment modules system to provision software to our users. To query whether a software is available, use
module spider <name_of_software>
Listed below are all the installed software as of 08/2022 on our system:
3seq
abaqus
abinit
abinit-epg
abyss
adf
admixmap
admixture
advisor
af4
afni
albacore
amber
amd
ancestrymap
anndata
annovar
ansys
ansysem
ants
arboreto
arcashla
aria2
arpack
arriba
aspeak
atacseq_harvard
ataqv
athlates
augustus
autodock_vina
awscli
azcopy
bamqc
bam-readcount
bamtools
bamutil
basespace
bash
bats
bazel
bbmap
bcbio-nextgen
bcftools
bcl2fastq2
beast
bedops
bedtools
berkeleygw
bioawk
biobambam2
bionano
bionano_tools
biopython
biotoolbox
bismark
bison
blast+
blender
bonito
boost
boost-compiled
bowtie
bowtie2
braker2
breseq
busco
bustools
bwa
bwa-mem2
bwtool
byobu
bzip2
cactus
cadence
cadical
caffe
calibre
cantera
canu
cap3
caper
causalml
cellphonedb
cellranger
cellranger-arc
cellranger-atac
cellxgene
chapel
checkm
chroma
chrome
chromedriver
circompara
circos
ciscall
cite-seq-count
clang
clark
clc-assembly-cell
clinker
clinqc
clonalframeml
cmake
cmappy
cnvkit
cnvnator
code-server
comsol
conn_toolbox
control-freec
convert3d
cooler
cosmosscope
cp2k
cpat
crimap
cromwell
ctpnet
cuba
cuda
cufflinks
curl
custom_waveview
customsim
cutadapt
cutruntools
cytoscape
damask
danpos2
dapars
datalad
dcm2niix
deepbinner
deeplabcut
deeptools
deepvariant
defuse
degnorm
delly
detonate
deviceQuery
diachromatic
diamond
discovardenovo
dms_tools2
doxygen
drop-seq
dsistudio
dx-toolkit
dynare
eagle
eclipidrmergepeaks
edirect
eigen
eman2
emboss
emmax
encfs
epacts
expat
fabtests
fanc
fastp
fastq_pair
fastq_screen
fastqc
fasttree
fastx-toolkit
fdtd
febio
ffmpeg
fftw
fhiaims
finesim
fish
fitsio
flashpca
flex
flye
fontconfig
fqtrim
freebayes
freefem
freesurfer
f-seq
fsl
fsleyes
fsps
fusioncatcher
fusion-inspector
gamess
gatb
gatk
gaussian
gblocks
gcc
gdal
gdc-tsv-tool
gdma
gdrcopy
genotypeharmonizer
genrich
geos
gfold
ghostscript
gistic
git
git-annex
github
glew
glimmer
glnexus
glpk
gmap-gsnap
gmsh
gnuplot
go
gomcl
google-cloud-sdk
googletest
gossamer
gotcloud
gpaw
gperf
grace
graphviz
gromacs
gsl
gubbins
gulp
guppy
gurobi
gym
hail
hclust
hdf5
hifive
hisat2
hmmer
homer
hpl
hspice
htseq
htslib
humann2
hydra
hypre
icount
idp
idp-fusion
idr
igv
imagej
imagemagick
indrops
infercnv
inspector
intel
intel-mpi
ipc
ipyrad
itk
iva
jaaba
jags
jansson
java
jbrowse2
jdftx
jellyfish
jmol
joe
julia
kaldi
kallisto
kentutils
kite
kneaddata
kpp
kraken2
krona
lammps
lapack
lc
lcov
ldpred
leafcutter
libevent
libfabric
libfaketime
libgtextutils
libjpeg
libpng
libtiff
libxc
libxml2
libzmq
lightgbm
lncfuntk
lofreq
lohhla
loompy
loomr
lua
luarocks
lumerical
macs
mafft
magicblast
magma
make
malt
manta
mapsplice2
masurca
mathematica
matlab
matlab-mcr
matlab-proxy
mauve
maven
medea
meerkat
mega2
megahit
megalodon
meme
merlin
meshlab
metabat2
metal
metaphlan
metis
mgltools
midnightcommander
minimac4
mira
mirdeep2
mirge
miso
mixcr
mkl
mmseqs2
modeller
modelsim
molden
molecularGSM
molpro
mongodb
mopac
mosek
mpich
mricrogl
mricron
mrtrix
mrtrix3
multinest
multiqc
mummer
muscle
mutsig
namd
nano
nanoplot
nauty
nccl
nektar
nektar++
neovim
netcdf
netpbm
neuron
nextflow
nextgenmap
nfcore
nf-core
ngmerge
ngsplot
ngsqc
nodejs
novocraft
nucleoatac
nvshmem
onedrive
openbabel
openblas
open-cravat
opencv
openfoam
openmolcas
openmpi
openslide-python
optitype
orca
osss-ucx
ovito
p7zip
packmol
paml
pandoc
pangolin
parallel
paraview
parmetis
parsplice
pathml
pcre
pda
peakdeck
peakseq
peaksplitter
pear
pedcheck
perl
petsc
petsc-gcc
pgi
phast
php
phylip
phyloacc
phyx
picard
pigz
pilon
pindel
piranha
pizzly
plink
plinkseq
plotjuggler
plumed
pmix
poltype
poppler
popt
porechop
postgresql
povray
primer3
prinseq
proj
prokka
proovread
provirus
psi4
pureclip
pvactools
pybedtools
pycharm
pychopper
pyrouge
pyscenic
python
pytorch
pytorch_gpu
qapa
qchem
qiime2
qorts
qt
qualimap
quantumespresso
quast
quickmirseq
r
racon
radia
rapsearch
raxml-ng
rclone
rdkit
readtools
reforge
regina
regtools
relion
rgt
rmats
rnachipintegrator
rnacocktail
rna-seqc
rnaseqmut
rosetta
rsem
rseqc
rstudio
rtg-core
s4
salmon
sambamba
samblaster
samstat
samtools
sas
scala
scanpy
scats
scbayes
seqcover
seqkit
seqspark
seqtk
shap
shapeit4
sicer
sickle
siesta
simpleitk
singularity
slurm
smoove
snakemake
snap-aligner
snpeff
snp-pileup
snptest
snver
snvmix2
soapindel
solar
somatic-sniper
sortmerna
sox
spaceranger
spades
spark
sparrow
spladder
spm
spreg
squashfs-tools
squid
sra-toolkit
srnanalyzer
star
star-fusion
star-seqr
stata
strelka
stringtie
structure
stubb
subread
surfaceGSM
svaba
svdetect
svviz2
synopsys
taiji
taiji-view
teaching
telescope
tensorflow
texlive
tinker
tmux
tokyo
tophat
torch
tpmcalculator
tracer
transdecoder
trf
trilinos
trimgalore
trimmomatic
trinity
trust
trust4
turbomole
ucsc-cell-browser
ucx
uintah
ultimaker-cura
umi-tools
unceqr
valgrind
vardictjava
varscan
vasp
vasp-vtst
vcf2maf
vcflib
vcftools
vcs
vdjtools
velocyto
velvet
venv
vep
vfs
vim
virtualgl
virtuoso-opensource
virus_detection_sra
virusfinder
virvarseq
visit
vlsi
vmd
vscode
vtk
vtune
vvp
westpa
wine
xhmm
xilinx/containers
xilinx/sdx
xilinx/vitis
xilinx/vivado
xtb
xz
zlib
zoltan