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list-of-software

List of Software

In general you can use the command module avail to show you the list of available software and their versions. Sometimes there are other software packages installed which aren't listed via the modules system; if you're curious you can look around in /export/apps to see if you can find what you're looking for.

Otherwise, here is a feeble attempt to list the software we have installed at ILRI, their versions, and (possibly) anyone who has experience running it. We endeavor to keep this list updated as the One True List™.

Name Latest version How to load Contact
abacas1.3.1module load abacas/1.3.1
abricate1.0.1module load abricate/1.0.1
abyss2.1.4module load abyss/2.1.4
ace1.01module load ace/1.01
ACT13.0.0module load act/13.0.0
admixture1.3.0module load admixture/1.3.0
AdapterRemoval1.5.4module load AdapterRemoval/1.5.4
aegean0.16.0module load aegean/0.16.0
aliview1.17.1module load aliview/1.17.1
amber suite12module load amber/12
ampssemblergit-51f0081module load ampssembler/git-51f0081
amos3.1.0module load amos/3.1.0
angsd0.910module load angsd/0.910
annovar2016-02-01module load annovar/2016-02-01
antismash7.0.0module load antismash/7.0.0
any2fasta0.4.2module load any2fasta/0.4.2
apt1.14.3module load apt/1.14.3
arb6.0.3module load arb/6.0.3
artemis16.0.0module load act/16.0.0
artic1.2.3module load artic/1.2.3
artic-tools0.3.1module load artic-tools/0.3.1
aspera-cli4.15.0module load aspera-cli/4.15.0
augustus3.3module load augustus/3.3
awscli2.4.0module load awscli/2
bam-readcount0.8.0module load bam-readcount/0.8.0
bamtools2.5.1module load bamtools/2.5.1
barrnap0.9module load barrnap/0.9
bayescan2.1module load bayescan/2.1
bbmap38.95module load bbmap/38.95
bcftools1.15.1module load bcftools/1.15.1
bcl2fastq2.20.0.422bcl2fastq
beagle3.1.2module load beagle/3.1.2
beast1.10.4module load beast/1.10.4
beast22.6.4module load beast2/2.6.4
bedops2.4.29module load bedops/2.4.29
bedtools2.29.0module load bedtools/2.29.0
binpacker1.0module load binpacker/1.0
bioperl1.7.2module load bioperl/1.7.2
bitseq0.7.5module load bitseq/0.7.5
blasrsmrtanalysis-4.0.0module load blasr/smrtanalysis-4.0.0
blast2.14.1+module load blast/2.14.1+
blobtools0.9.19.3module load blobtools/0.9.19.3
blat37x1module load blat/37x1
bmtagger0.3.102.4module load bmtagger/0.3.102.4
bowtie11.2.3module load bowtie/1.2.3
bowtie22.5.0module load bowtie2/2.5.0
brig0.95module load brig/0.95
BUSCO 5.2.2module load BUSCO/5.2.2
bwa0.7.17module load bwa/0.7.17
cafe4.1module load cafe/4.1
cangs1.1module load cangs/1.1
canu1.8module load canu/1.8
cap3latestmodule load cap3/latest
ccmetagen1.4.0module load ccmetagen/1.4.0
cd-hit4.8.1module load cd-hit/4.8.1
cegmav2.5module load cegma/v2.5
cgmlst-dists0.4.0module load cgmlst-dists/0.4.0
celera-wgs6.1module load celera-wgs/6.1
censor4.2.28module load censor/4.2.28
centrifuge1.0.4module load centrifuge/1.0.4
changeo1.2.0module load changeo/1.2.0
checkm1.1.2module load checkm/1.1.2
chewbbacagit-87102063module load chewbbaca/git-87102063
circos0.69-9module load circos/0.69-9
clonalframe1.2module load clonalframe/1.2
clonalframeml1.0module load clonalframeml/1.0
clustalw2.1module load clustalw/2.1
CNVnator0.3.3module load CNVnator/0.3.3
consed20.0module load consed/20.0
cooler0.8.10module load cooler/0.8.10
COPEread1.1.2module load coperead/1.1.2
corset1.06module load corset/1.06
cufflinks2.2.1module load cufflinks/2.2.1
cutadapt3.5module load cutadapt/3.5
czid-cli3.0.2module load czid-cli/3.0.2
dextractorgit-a7f50c52module load dextractor/git-a7f50c52
dendroscope2.7.4module load dendroscope/2.7.4
diamond2.0.14module load diamond/2.0.14
disty0.1.0module load disty/0.1.0
dorado0.5.0module load dorado/0.5.0
drep2.5.4module load drep/2.5.4
ea-utils1.04.807module load ea-utils/1.04.807
eagle2.4.1module load eagle/2.4.1
edirect 7.80 module load edirect/7.80
eggnog-mapper 2.1.9 module load eggnog-mapper/2.1.9
eigenstrat3.0module load eigenstrat/3.0
emblmygff32.1module load emblmygff3/2.1
emboss6.6.0module load emboss/6.6.0
easer1.7.0module load easer/1.7.0
est2unilatestmodule load est2uni/latest
exabayes1.4.1module load exabayes/1.4.1
express1.5.1module load express/1.5.1
falco0.3.0module load falco/0.3.0
falcon-phasegit-7c50154emodule load falcon-phase/git-7c50154e
fastANI1.3module load fastANI/1.3
fastp0.22.0module load fastp/0.22.0
fastPHASE1.4.8module load fastPHASE/1.4.8
fastqc0.11.9module load fastqc/0.11.9
fastSTRUCTURE1.0module load fastSTRUCTURE/1.0
fasttree2.1.11module load fasttree/2.1.11
fastx_toolkit0.0.13module load fastx_toolkit/0.0.13
figarogit-337aa9module load figaro/git-337aa9
figtree1.4.0module load figtree/1.4.0
flapjack 1.18.04.23-betamodule load flapjack/1.18.04.23-beta
flash 1.2.11module load FLASH/1.2.11
flash2git-64826f45module load flash2/git-64826f45
flexbar2.7.0module load flexbar/2.7.8
flux-capacitor1.6.1module load flux-capacitor/1.6.1
flye2.9module load flye/2.9
frappe1.1module load frappe/1.1
FragGeneScan 1.30module load fraggenescan/1.30
freebayes1.3.4module load freebayes/1.3.4
funannotate1.8.15See software page
GassFlow 1.0module load gassflow/1.0
gatk4.4.0.0module load gatk/4.4.0.0
gapfiller1.10module load gapfiller/1.10
geneid1.4.4module load geneid/1.4.4
genometools1.6.1module load genometools/1.6.1
genomeworksgit-baab5668module load genomeworks/git-baab5668
genscanlatestmodule load genscan/latest
gffread0.9.6module load gffread/0.9.6
glimmer3.02module load glimmer/3.02
glu1.0b3-prerelease4module load glu/1.0b3-prerelease4
gmap2015-12-31module load gmap/2015-12-31
graphlan1.1.3module load graphlan/1.1.3
graphmap0.5.2module load graphmap/0.5.2
grom-rd1.0module load grom-rd/1.0
gromacs2018.2module load gromacs/2018.2
groovy2.4.9module load groovy/2.4.9
GSEA2.2.3module load gsea/2.2.3
gtdbtk1.1.1module load gtdbtk/1.1.1
guidance2.02module load guidance/2.02
guppy6.2.1module load guppy/6.2.1
halcyon0.1.1module load halcyon/0.1.1
hapflk1.4module load hapflk/1.4
hapmix2.0module load hapmix/2.0
hawkgit-a177811dmodule load hawk/git-a177811d
hclust21.0.0module load hclust2/1.0.0
hdf51.8.19module load hdf5/1.8.19
hmmer3.3module load hmmer/3.3
hmmIBD2.0.4module load hmmIBD/2.0.4
hpg-variant1.0module load hpg-variant/1.0
hic_qcgit-1e132fb2module load hic_qc/git-1e132fb2
hifiasm0.16.1module load hifiasm/0.16.1
hisat22.1.0module load hisat2/2.1.0
htseq0.9.1module load htseq/0.9.1
htslib1.15.1module load htslib/1.15.1
hypo1.0.3module load hypo/1.0.3
hyphy2.5.48module load hyphy/2.5.48
idba1.1.2module load idba/1.1.2
igblast1.10.0module load igblast/1.10.0
igdiscover0.12.3module load igdiscover/0.12.3
igrec3.0.0module load igrec/3.0.0
igsimulatorgit-c3778b74module load igsimulator/git-c3778b74
iqtree2.2.0module load iqtree/2.2.0
igv2.4.5module load igv/2.4.5
igvtools2.3.98module load igvtools/2.3.98
infernal1.1.2module load infernal/1.1.2
integron-finder2.0.2module load integron-finder/2.0.2
interproscan5.13module load interproscan/5.13
i-tasserlatestmodule load i-tasser/latest
ivar1.3.1module load ivar/1.3.1
jellyfish2.3.0module load jellyfish/2.3.0
jMHC1.5.0929module load jMHC/1.5.0929
juicebox1.11.08module load juicebox/1.11.08
juicer1.6module load juicer/1.6
kaiju1.8.2module load kaiju/1.8.2
kallisto0.43.0module load kallisto/0.43.0
karect1.0module load karect/1.0
kat2.3.4module load kat/2.3.4
kma1.4.11module load kma/1.4.11
kmc3.1.1module load kmc/3.1.1
kmerfreqgit-90fca00dmodule load kmerfreq/git-90fca00d
kmergenie1.7038module load kmergenie/1.7038
kmer-ssrgit-4043c0e7module load kmer-ssr/git-4043c0e7
kraken2.1.2module load kraken/2.1.2
krona2.8.1module load krona/2.8.1
lamp2.5module load lamp/2.5
lava0.1module load lava/0.1
ldhat2.1module load ldhat/2.1
libsvm3.20module load libsvm/3.20
lighter1.1.2module load lighter/1.1.2
longshot0.4.5module load longshot/0.4.5
lordec0.9module load lordec/0.9
ltr_retriever2.9.0module load ltr_retriever/2.9.0
lucy1.19pmodule load lucy/1.19p
mafft7.505module load mafft/7.505
maker3.01.03module load maker/3.01.03
mapsplice2.2.0module load mapsplice/2.2.0
marginaligngit-2369dafdmodule load marginalign/git-2369dafd
marginpolish1.0.0module load marginpolish/1.0.0
mash2.2module load mash/2.2
masurca4.1.0module load masurca/4.1.0
mauve2.3.1module load mauve/2.3.1
maxbin22.2.7module load maxbin2/2.2.7
maximus0.2module load maximus/0.2
mcl14-137module load mcl/14-137
mcscanxgit-97e74f40module load mcscanx/git-97e74f40
MECATgit-d04bfa84module load MECAT/git-d04bfa84
medaka1.4.3module load medaka/1.4.3
megahit1.2.9module load megahit/1.2.9
megan4.70.4module load megan/4.70.4
megax10.0.5module load megax/10.0.5
metabat2.12.1module load metabat/2.12.1
metaeukgit-9818d1a5module load metaeuk/git-9818d1a5
metaphlan4.0.6module load metaphlan/4.0.6
metis5.1.0module load metis/5.1.0
migec1.2.4amodule load migec/1.2.4a
migmap1.0.2module load migmap/1.0.2
miniasm0.3module load miniasm/0.3
minimac32.0.1module load minimac3/2.0.1
minimac41.0.3module load minimac4/1.0.3
minimap22.24module load minimap2/2.24
MinPath1.0.2module load MinPath/1.2
mira4.0.2module load mira/4.0.2
mirdeep20.1.3module load mirdeep2/0.1.3
mitools1.4module load mitools/1.4
mixcr3.0.11module load mixcr/3.0.11
mkatari-ilrilatestmodule load mkatari-ilri/latest
modeller9.17module load modeller/9.17
mosdepth0.2.9module load mosdepth/0.2.9
mothur1.44.1module load mothur/1.44.1
mothur-kronagit-87499a0module load mothur-krona/git-87499a0
mpiblast1.6.0module load mpiblast/1.6.0
mrbayes3.2.7amodule load mrbayes/3.2.7a
multiqc1.12module load multiqc/1.12
muscle3.8.1551module load muscle/3.8.1551
mummer4.0.0rc1module load mummer/4.0.0rc1
nanopolish0.14.0module load nanopolish/0.14.0
nanoqcgit-a7bcbdcemodule load nanoqc/git-a7bcbdce
netmhcpan2.8module load netmhcpan/2.8
nextalign1.11.0module load nextalign/1.11.0
nextclade2.11.0module load nextclade/2.11.0
nextclip1.3.1module load nextclip/1.3.1
nextflow23.10 (23.10.0)module load nextflow/23.10
ngs-tools3.0.0module load ngs-tools/3.0.0
ntCard1.0.0module load ntCard/1.0.0
ngmlr0.2.7module load ngmlr/0.2.7
ngsqctoolkit2.3.3module load ngsqctoolkit/2.3.3
nQuiregit-a990a88emodule load nQuire/git-a990a88e
novacraft3.02.07module load novacraft/3.02.07
oases0.2.08module load oases/0.2.08
ocaml4.02.1module load ocaml/4.02.1
oligoarrayaux3.8.1module load oligoarrayaux/3.8.1
opam1.2.0module load opam/1.2.0
orthomcl2.0.3module load orthomcl/2.0.3
Oyster River Protocol2.2.8module load orp/2.2.8
pagan0.61module load pagan/0.61
pairfq0.14.4module load pairfq/0.14.4
paml4.9amodule load paml/4.9a
panaroo1.3.3module load panaroo/1.3.3
pandaseq2.8.1module load pandaseq/2.8.1
pastad939adb2module load pasta/d939adb2
pathoscope2.0.7module load pathoscope/2.0.7
pear0.9.6module load pear/0.9.6
pblat2.1module load pblat/2.1
pbsuite15.8.24module load pbsuite/15.8.24
perl5.28.2module load perl/5.28.2
PGDSpider2.1.1.0module load pgdspider/2.1.1.0
phrap1.080812module load phrap/1.080812
phred0.990722.fmodule load phred/0.990722.f
phylip3.696module load phylip/3.696
phyml3.3.20180621module load phyml/3.3.20180621
picard2.27.5module load picard/2.27.5
picrust1.0.0module load picrust/1.0.0
pilon1.23module load pilon/1.23
plasmidid1.6.5module load plasmidid/1.6.5
platanus1.2.1module load platanus/1.2.1
plink2.00-alphamodule load plink/2.00-alpha
pod50.3.2module load pod5/0.3.2
polyphen2.2.2module load polyphen/2.2.2
poplddecay3.41module load poplddecay/3.41
porechop0.3.2premodule load porechop/0.3.2pre
pplacer1.1.alpha19module load pplacer/1.1.alpha19
prank170427module load prank/170427
presto0.5.13module load presto/0.5.13
primalscheme1.3.2module load primalscheme/1.3.2
primer32.3.6module load primer3/2.3.6
prinseq0.20.4module load prinseq/0.20.4
prodigal2.6.3module load prodigal/2.6.3
prokka1.14.6module load prokka/1.14.6
provean1.1.5module load provean/1.1.5
purge_haplotigs1.1.1module load purge_haplotigs/1.1.1
python3.9.17module load python/3.9
qdd3_betamodule load qdd/3_beta
qiime1.9.1module load qiime/1.9.1
qiime22021.8module load qiime2/2021.8
quast5.0.2module load quast/5.0.2
quickmerge0.3module load quickmerge/0.3
Quorum1.1.1module load quorum/1.1.1
R4.3.1module load R/4.3
racon1.5.0module load racon/1.5.0
rapsearch2.22module load rapsearch/2.22
RATTr18module load ratt/r18
RAxML8.2.12module load RAxML/8.2.12
ray2.3.1module load ray/2.3.1
rcorrector1.0.5module load rcorrector/1.0.5
RDP Classifier2.11module load rdp-classifier/2.11
recon1.08module load recon/1.08
repeatmasker4.1.2-p1module load repeatmasker/4.1.2-p1
repeatmodeler2.0.1module load repeatmodeler/2.0.1
repseqio1.3.3module load repseqio/1.3.3
rgi6.0.2module load rgi/6.0.2
rmblast2.11.0module load rmblast/2.11.0
roary3.13.0module load roary/3.13.0
root6.08.06module load root/6.08.06
rRNASelector1.1module load rrnaselector/1.1
RSEM1.3.1module load RSEM/1.3.1
rseqc2.6.4module load rseqc/2.6.4
ruby3.1 (3.1.4)module load ruby/3.1
samtools1.15.1module load samtools/1.15.1
sailfish0.9.2module load sailfish/0.9.2
salmon1.3.0module load salmon/1.3.0
salsagit-974589f3module load salsa/git-974589f3
satsuma2git-37c5f386module load satsuma2/git-37c5f386
scipio1.4.1module load scipio/1.4.1
scythe0.994-betamodule load scythe/0.994-beta
sepp4.5.1module load sepp/4.5.1
seroba1.0.0module load seroba/1.0.0
seq_crumbs0.1.8module load seq_crumbs/0.1.8
seqkit0.11.0module load seqkit/0.11.0
seqqsgit-3d053750module load seqqs/git-3d053750
seqtk1.3module load seqtk/1.3
seqwish0.6module load seqwish/0.6
shannon0.0.2module load shannon/0.0.2
shannon_cpp0.5.0module load shannon_cpp/0.5.0
shapeit2.904module load shapeit/2.904
shasta0.4.0module load shasta/0.4.0
sickle1.33module load sickle/1.33
sift4.0.3bmodule load sift/4.0.3b
sistr1.0.2module load sistr/1.0.2
smalt0.7.6module load smalt/0.7.6
smartdenovogit-5cc1356bmodule load smartdenovo/git-5cc1356b
snakemake6.15.5module load snakemake/6.15
sniffles1.0.12bmodule load sniffles/1.0.12b
snippy4.6.0module load snippy/4.6.0
snowhite1.1.4module load snowhite/1.1.4
snpeff5.1module load snpeff/5.1
snpmeta2.0module load snpmeta/2.0
snp-pipeline1.0.1module load snp-pipeline/1.0.1
SOAPdenovo2git-c4d2f5eemodule load SOAPdenovo2/git-c4d2f5ee
SOAPaligner2.21module load SOAPaligner/2.21
SOAPsnp1.03module load SOAPsnp/1.03
SOAPsplice1.10module load SOAPsplice/1.10
SOAPdenovo-Trans1.03module load SOAPdenovo-Trans/1.03
SolexaQA++3.1.3module load SolexaQA++/3.1.3
spades3.15 (3.15.5)module load spades/3.15
sourmash1.0module load sourmash/1.0
speedseq0.1.2module load speedseq/0.1.2
splitstree4.11.3module load splitstree/4.11.3
spread1.0.6module load spread/1.0.6
squid1.9gmodule load squid/1.9g
sratoolkit2.10.0module load sratoolkit/2.10.0
sra-tools3.0.0module load sra-tools/3.0.0
srprism3.1.2module load srprism/3.1.2
srst2git-73f885f5module load srst2/git-73f885f5
sspace3.0module load sspace/3.0
sspace-longread1.1module load sspace-longread/1.1
stacks2.62module load stacks/2.62
staden2.0.0b8module load staden/2.0.0b8
star2.7.10amodule load star/2.7.10a
structure2.3.4module load structure/2.3.4
stringtie1.3.4dmodule load stringtie/1.3.4d
stringtie22.2.1module load stringtie2/2.2.1
subread1.6.2module load subread/1.6.2
svmlightV6.02module load svmlight/V6.02
tabixgit-76b4bbdfmodule load tabix/git-76b4bbdf
tablet1.17.08.17module load tablet/1.17.08.17
tassel5.2.77module load tassel/5.2.77
tmiseq2016-01-31module load tmiseq/2016-01-31
tophat2.1.0module load tophat2/2.1.0
tracer1.6module load tracer/1.6
transabyss2.0.1module load transabyss/2.0.1
TransDecoder2.0.1module load TransDecoder/2.0.1
Transrate1.0.3module load transrate/1.0.3
trf4.0.9module load trf/4.0.9
trimgalore0.6.7module load trimgalore/0.6.7
trimmomatic0.39module load trimmomatic/0.39
trinityv2.11.0module load trinity/v2.11.0
trinotate2.0.2module load trinotate/2.0.2
twinscan3.5module load twinscan/3.5
umi-tools 0.2.3 module load umi-tools/0.2.3
unicycler 0.4.0 module load unicycler/0.5.0
usearch v7.0.1090 module load usearch/v7.0.1090
varscan2.4.2module load varscan/2.4.2
vcfdogit-508cc19bmodule load vcfdo/git-508cc19b
vcflibgit-7f1575emodule load vcflib/git-7f1575e
vcftools0.1.16module load vcftools/0.1.16
velvet1.2.10-kmer111module load velvet/1.2.10-kmer111
velvetoptimiser2.2.6module load velvetoptimiser/2.2.6
vep109.3module load vep/109.3
vg1.27.0module load vg/1.27.0
viennarna2.4.14module load viennarna/2.4.14
virusdetect1.7module load virusdetect/1.7
vntrseek1.08module load vntrseek/1.08
vsearch2.8.0module load vsearch/2.8.0
w2rapgit-60781b6cmodule load w2rap/git-60781b6c
w2rap-contiggergit-a43f5a05module load w2rap-contigger/git-a43f5a05
whatshap0.16module load whatshap/0.16
wise2.4.1module load wise/2.4.1
wombat2020-02-07module load wombat/2020-02-07
wtdbg22.4module load wtdbg2/2.4

The source code for all environment modules can be found in ILRI's GitHub repository.

list-of-software.txt · Last modified: 2023/12/18 08:55 by aorth