User Tools

Site Tools


list-of-software

This is an old revision of the document!


abacas|1.3.1|''module load abacas/1.3.1''| | |[[abricate-software|abricate|1.0.1|module 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
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
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
bcftools1.13module load bcftools/1.13
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
blast2.12.0+module load blast/2.12.0+
blobtools0.9.19.3module load blobtools/0.9.19.3
blat06-Aug-2013module load blat/06-Aug-2013
bowtie1 1.2.3module load bowtie/1.2.3
bowtie2 2.3.4.1module load bowtie2/2.3.4.1
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
cd-hit4.8.1module load cd-hit/4.8.1
cegmav2.5module load cegma/v2.5
celera-wgs6.1module load celera-wgs/6.1
censor4.2.28module load censor/4.2.28
centrifuge1.0.4module load centrifuge/1.0.4
changeo1.0.0module load changeo/1.0.0
checkm1.1.2module load checkm/1.1.2
circos0.69-9module load circos/0.69-9
clonalframe1.2module load clonalframe/1.2
clonalframeml1.0module load clonalframeml/1.0
clustalo1.2.3module load clustalo/1.2.3
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
diamond0.9.9module load diamond/0.9.9
drep2.5.4module load drep/2.5.4
ea-utils1.04.807module load ea-utils/1.04.807
edirect 7.80 module load edirect/7.80
eigenstrat3.0module load eigenstrat/3.0
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
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
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
funannotate1.8.7module load funannotate/1.8.7
GassFlow 1.0module load gassflow/1.0
gatk4.2.2.0module load gatk/4.2.2.0
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
guppy5.0.11module load guppy/5.0.11
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
hisat22.1.0module load hisat2/2.1.0
htseq0.9.1module load htseq/0.9.1
htslib1.13module load htslib/1.13
hypo1.0.3module load hypo/1.0.3
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
iqtree1.6.12module load iqtree/1.6.12
igv2.4.5module load igv/2.4.5
igvtools2.3.98module load igvtools/2.3.98
infernal1.1.2module load infernal/1.1.2
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
kma1.4.0module load kma/1.4.0
kmc3.1.1module load kmc/3.1.1
kmergenie1.7038module load kmergenie/1.7038
kmer-ssrgit-4043c0e7module load kmer-ssr/git-4043c0e7
kraken2.0.8-betamodule load kraken/2.0.8-beta
krona2.4module load krona/2.4
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
lordec0.9module load lordec/0.9
ltr_retriever2.9.0module load ltr_retriever/2.9.0
lucy1.19pmodule load lucy/1.19p
mafft7.475module load mafft/7.475
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
masurca3.3.1module load masurca/3.3.1
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
metaphlan3.0.13module load metaphlan/3.0.13
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
minimap22.22module load minimap2/2.22
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
mrbayes3.2.2module load mrbayes/3.2.2
multiqc1.6module load multiqc/1.6
muscle3.8.1551module load muscle/3.8.1551
mummer4.0.0rc1module load mummer/4.0.0rc1
nanopolish0.10.2module load nanopolish/0.10.2
netmhcpan2.8module load netmhcpan/2.8
nextalign1.3.0module load nextalign/1.3.0
nextclade1.3.0module load nextclade/1.3.0
nextclip1.3.1module load nextclip/1.3.1
nextflow21.10 (21.10.6)module load nextflow/21.10
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
nvtop1.2.2module load nvtop/1.2.2
novacraft3.02.07module load novacraft/3.02.07
oases0.2.08module load oases/0.2.08
ocaml4.02.1module load ocaml/4.02.1
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
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
picard2.26.1module load picard/2.26.1
picrust1.0.0module load picrust/1.0.0
pilon1.23module load pilon/1.23
plasmidid1.6.3module load plasmidid/1.6.3
platanus1.2.1module load platanus/1.2.1
plink2.00-alphamodule load plink/2.00-alpha
polyphen2.2.2module load polyphen/2.2.2
poplddecay3.41module load poplddecay/3.41
porechop0.2.4module load porechop/0.2.4
pplacer1.1.alpha19module load pplacer/1.1.alpha19
prank170427module load prank/170427
presto0.5.13module load presto/0.5.13
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
python3.8.11module load python/3.8
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
R4.0.5module load R/4.0
racon1.3.1module load racon/1.3.1
rmblast2.11.0module load rmblast/2.11.0
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
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
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
ruby2.2.3module load ruby/2.2.3
samtools1.13module load samtools/1.13
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
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
snowhite1.1.4module load snowhite/1.1.4
SnpEff & SnpSift4.1gmodule load snpeff/4.1g
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 (3.15.4)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
sspace3.0module load sspace/3.0
sspace-longread1.1module load sspace-longread/1.1
stacks1.24module load stacks/1.24
staden2.0.0b8module load staden/2.0.0b8
star2.7.1amodule load star/2.7.1a
structure2.3.4module load structure/2.3.4
stringtie1.3.4dmodule load stringtie/1.3.4d
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
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 0.4.7 module load unicycler/0.4.7
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
vep92.1module load vep/92.1
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.1647001924.txt.gz · Last modified: 2022/03/11 12:32 by aorth