abacas
abra2
abricate/summary
abritamr/run
adapterremoval
adapterremovalfixprefix
admixture
affy/justrma
agat/convertbed2gff
agat/convertgff2bed
agat/convertspgff2gtf
agat/convertspgff2tsv
agat/convertspgxf2gxf
agat/spaddintrons
agat/spextractsequences
agat/spfilterbyorfsize
agat/spfilterfeaturefromkilllist
agat/spflagshortintrons
agat/spkeeplongestisoform
agat/spmergeannotations
agat/spstatistics
agat/sqstatbasic
agrvate
ale
allelecounter
ampcombi
ampcombi2/cluster
ampcombi2/complete
ampcombi2/parsetables
ampir
amplify/predict
amps
amrfinderplus/run
amrfinderplus/update
amulety/antiberta2
amulety/antiberty
amulety/balmpaired
amulety/esm2
angsd/contamination
angsd/docounts
angsd/gl
anndata/barcodes
anndata/getsize
annosine
annotsv/annotsv
annotsv/installannotations
anota2seq/anota2seqrun
antismash/antismash
antismash/antismashdownloaddatabases
antismash/antismashlite
antismash/antismashlitedownloaddatabases
arcashla/extract
argnorm
aria2
ariba/getref
ariba/run
arriba/arriba
arriba/download
arriba/visualisation
artic/aligntrim
artic/guppyplex
artic/minion
art/illumina
ascat
ataqv/ataqv
ataqv/mkarv
atlas/call
atlasgeneannotationmanipulation/gtf2featureannotation
atlas/pmd
atlas/recal
atlas/splitmerge
authentict/deam2cont
backsub
bacphlip
bakta/bakta
bakta/baktadbdownload
bam2fastx/bam2fastq
bamaligncleaner
bamclipper
bamreadcount
bamtofastq10x
bamtools/convert
bamtools/split
bamtools/stats
bamutil/clipoverlap
bamutil/trimbam
barrnap
basicpy
bbmap/align
bbmap/bbduk
bbmap/bbmerge
bbmap/bbnorm
bbmap/clumpify
bbmap/filterbyname
bbmap/index
bbmap/pileup
bbmap/repair
bbmap/sendsketch
bff
bioawk
biohansel
biomformat/convert
biscuit/align
biscuit/biscuitblaster
biscuit/bsconv
biscuit/epiread
biscuit/index
biscuit/mergecg
biscuit/pileup
biscuit/qc
biscuit/vcf2bed
bismark/coverage2cytosine
bismark/deduplicate
bismark/genomepreparation
bismark/methylationextractor
bismark/report
bismark/summary
blat
bowtie/align
bowtie/build
bracken/build
bracken/combinebrackenoutputs
braker3
bwameth/align
bwameth/index
cafe
calder2
canu
celesta
cellbender/merge
cellbender/removebackground
cellrangerarc/count
cellrangerarc/mkfastq
cellrangerarc/mkgtf
cellrangerarc/mkref
cellrangeratac/count
cellrangeratac/mkfastq
cellrangeratac/mkref
cellranger/count
cellranger/mkgtf
cellranger/mkref
cellranger/mkvdjref
cellranger/multi
cellranger/vdj
cellsnp/modea
centrifuge/build
centrifuge/centrifuge
centrifuge/kreport
checkm/lineagewf
checkm/qa
checkv/downloaddatabase
checkv/endtoend
checkv/updatedatabase
chewbbaca/allelecall
chewbbaca/createschema
chopper
chromap/chromap
chromap/index
circexplorer2/annotate
circexplorer2/parse
circularmapper/circulargenerator
clair3
clame
clippy
clonalframeml
clustalo/guidetree
cmseq/polymut
cnaqc
cnvkit/access
cnvkit/antitarget
cnvkit/batch
cnvkit/call
cnvkit/export
cnvkit/genemetrics
cnvkit/reference
cnvkit/target
cnvpytor/callcnvs
cnvpytor/histogram
cnvpytor/importreaddepth
cnvpytor/partition
cnvpytor/view
cobrameta
cobs/classicconstruct
cobs/compactconstruct
comebin/runcomebin
concoct/concoct
concoct/concoctcoveragetable
concoct/cutupfasta
concoct/extractfastabins
concoct/mergecutupclustering
conifer
cooltools/eigscis
coptr/estimate
coptr/extract
coptr/index
coptr/map
coptr/merge
coreograph
coverm/contig
coverm/genome
cowpy
crabs/import
crabs/insilicopcr
cramino
crisprcleanr/normalize
crispresso2
crumble
csvtk/concat
csvtk/join
csvtk/sort
csvtk/split
ctatsplicing/prepgenomelib
ctatsplicing/startocancerintrons
ctree
custom/catadditionalfasta
custom/dumpsoftwareversions
custom/filterdifferentialtable
custom/getchromsizes
custom/gtffilter
custom/matrixfilter
custom/tabulartogseachip
custom/tabulartogseacls
custom/tabulartogseagct
custom/tx2gene
cutesv
damageprofiler
dastool/scaffolds2bin
decoupler/decoupler
dedup
deeparg/downloaddata
deeparg/predict
deepbgc/download
deepbgc/pipeline
deepcell/mesmer
deepsomatic
deeptmhmm
deepvariant
deseq2/differential
diamond/blastp
diamond/blastx
diamond/cluster
diamond/makedb
diann
diann/insilicolibrarygeneration
doubletdetection
dragen/germline
dragonflye
drep/compare
drep/dereplicate
dshbio/exportsegments
dshbio/filterbed
dshbio/filtergff3
dshbio/splitbed
dshbio/splitgff3
dssp/mkdssp
duphold
dupradar
dysgu/run
eagle2
ectyper
eido/convert
eido/validate
eigenstratdatabasetools/eigenstratsnpcoverage
eklipse
emboss/cons
emboss/revseq
emboss/seqret
emmtyper
endorspy
entrezdirect/esearch
entrezdirect/esummary
entrezdirect/xtract
epang/place
epang/split
estsfs
evigene/tr2aacds
expansionhunterdenovo/merge
expansionhunterdenovo/profile
falint
famsa/guidetree
faqcs
fargene
fast2q
fastavalidator
fastcov
fastme
fastqe
fastqscan
fasttree
fastx/collapser
fcs/fcsadaptor
fcs/fcsgx
fcsgx/cleangenome
fcsgx/fetchdb
fcsgx/rungx
ffq
fibertoolsrs/addnucleosomes
fibertoolsrs/extract
fibertoolsrs/predictm6a
find/concatenate
find/unpigz
flash
foldcomp/compress
foldcomp/decompress
foldmason/createdb
foldmason/msa2lddtreport
foldseek/createdb
foldseek/easysearch
fq/generate
fusioncatcher/build
fusioncatcher/fusioncatcher
fusioninspector
fusionreport/detect
fusionreport/download
gamma/gamma
gangstr
ganon/buildcustom
ganon/classify
ganon/report
ganon/table
gappa/examineassign
gappa/examinegraft
gappa/examineheattree
gatk/indelrealigner
gatk/realignertargetcreator
gatk/unifiedgenotyper
gecco/convert
gecco/run
gem2/gem2bedmappability
gem2/gemindexer
gem2/gemmappability
gem3/gem3indexer
gem3/gem3mapper
genescopefk
genmap/index
genmap/map
genomad/download
genomad/endtoend
genotyphi/parse
genrich
geofetch
geoquery/getgeo
getorganelle/config
getorganelle/fromreads
gfaffix
gffcompare
gget/gget
gmmdemux
goat/taxonsearch
goleft/indexcov
goleft/indexsplit
gprofiler2/gost
grabix/check
graphmap2/align
graphmap2/index
graphtyper/genotype
graphtyper/vcfconcatenate
gsea/gsea
gstama/collapse
gstama/merge
gstama/polyacleanup
gt/gff3
gt/gff3validator
gt/ltrharvest
gt/stat
gt/suffixerator
gunc/downloaddb
gunc/mergecheckm
gunc/run
gvcftools/extractvariants
gzrt
hamronization/abricate
hamronization/amrfinderplus
hamronization/deeparg
hamronization/fargene
hamronization/rgi
hamronization/summarize
hapibd
haplocheck
haplogrep2/classify
happy/ftxpy
hasheddrops
helitronscanner/draw
helitronscanner/scan
hhsuite/hhblits
hhsuite/hhsearch
hicap
hificnv
hiphase
hlala/preparegraph
hlala/typing
hmmer/eslalimask
hmmer/eslreformat
hmmer/hmmalign
hmmer/hmmbuild
hmmer/hmmfetch
hmmer/hmmpress
hmmer/hmmrank
hmmer/hmmsearch
hmmer/jackhmmer
hmtnote/annotate
homer/annotatepeaks
homer/findpeaks
homer/maketagdirectory
homer/makeucscfile
homer/pos2bed
hostile/clean
hostile/fetch
hpsuissero
htodemux
htseq/count
htsnimtools/vcfcheck
humid
hypo
ichorcna/createpon
ichorcna/run
icountmini/metagene
icountmini/peaks
icountmini/segment
icountmini/sigxls
icountmini/summary
idemux
idr
igv/js
igvreports
ilastik/multicut
ilastik/pixelclassification
immunedeconv
infernal/cmsearch
instrain/compare
instrain/profile
integronfinder
iphop/download
iphop/predict
iqtree
irescue
islandpath
ismapper
isoseq3/tag
isoseq/cluster
isoseq/refine
ivar/consensus
ivar/trim
ivar/variants
jellyfish/count
jellyfish/dump
jupyternotebook
jvarkit/dict2bed
jvarkit/sam2tsv
jvarkit/vcf2table
jvarkit/vcffilterjdk
jvarkit/vcfpolyx
jvarkit/wgscoverageplotter
kaiju/kaiju
kaiju/kaiju2krona
kaiju/kaiju2table
kaiju/mergeoutputs
kaiju/mkfmi
kallistobustools/count
kallistobustools/ref
kat/hist
khmer/normalizebymedian
khmer/trimlowabund
khmer/uniquekmers
kleborate
kma/index
kma/kma
kmcp/compute
kmcp/index
kmcp/merge
kmcp/profile
kmcp/search
kofamscan
kraken2/add
kraken2/build
kraken2/buildstandard
krakentools/combinekreports
krakentools/extractkrakenreads
krakentools/kreport2krona
krakenuniq/build
krakenuniq/download
krakenuniq/preloadedkrakenuniq
krona/kronadb
krona/ktimportkrona
krona/ktimporttaxonomy
krona/ktimporttext
krona/ktupdatetaxonomy
learnmsa/align
leehom
legsta
leviosam2/index
leviosam2/lift
limma/differential
lissero
lofreq/alnqual
lofreq/call
lofreq/callparallel
lofreq/filter
lofreq/indelqual
lofreq/somatic
lofreq/viterbi
longphase/haplotag
longphase/phase
longstitch
lsa/cosine
ltrfinder
ltrharvest
ltrretriever/lai
ltrretriever/ltrretriever
macrel/contigs
macs2/callpeak
macs3/callpeak
mafft/guidetree
mageck/count
mageck/mle
mageck/test
magus/guidetree
malt/build
maltextract
malt/run
mapad/index
mapad/map
mapdamage2
mash/dist
mashmap
mash/screen
mash/sketch
mashtree
maxbin2
maxquant/lfq
mcquant
mcroni
mcstaging/imc2mc
mcstaging/phenoimager2mc
mdust
medaka
megan/daa2info
megan/rma2info
melon
meningotype
merfin/hist
metabat2/jgisummarizebamcontigdepths
metacache/build
metacache/query
metaeuk/easypredict
metamaps/classify
metamaps/mapdirectly
metaphlan3/mergemetaphlantables
metaphlan3/metaphlan3
metaphlan/makedb
metaphlan/mergemetaphlantables
metaphlan/metaphlan
metaspace/converter
metaspace/download
methbat/profile
methyldackel/extract
methyldackel/mbias
midas/run
mindagap/duplicatefinder
mindagap/mindagap
minia
miniprot/align
miniprot/index
miranda
mirdeep2/mapper
mirdeep2/mirdeep2
mirtop/counts
mirtop/export
mirtop/gff
mirtop/stats
mirtrace/qc
mlst
mobster
mobsuite/recon
molkartgarage/clahe
motus/downloaddb
motus/merge
motus/preplong
motus/profile
msisensor/msi
msisensor/scan
mtnucratio
mudskipper/bulk
mudskipper/index
multiseqdemux
mummer
muscle
mygene
mykrobe/predict
myloasm
nacho/normalize
nacho/qc
nail/search
nanocomp
nanofilt
nanolyse
nanomonsv/parse
nanoplot
narfmap/hashtable
ncbigenomedownload
ncbitools/vecscreen
nextclade/datasetget
nextclade/run
nextgenmap
ngmaster
ngmerge
ngsbits/bedannotategc
ngsbits/bedcoverage
ngsbits/updhunter
nonpareil/curve
nonpareil/nonpareil
nonpareil/nonpareilcurvesr
nonpareil/set
nucmer
odgi/build
odgi/draw
odgi/layout
odgi/sort
odgi/squeeze
odgi/stats
odgi/unchop
odgi/view
odgi/viz
oncocnv
openms/idmassaccuracy
opt/flip
optitype
opt/stat
opt/track
orthofinder
osfclient/fetch
paftools/sam2paf
pairix
pairtools/dedup
pairtools/flip
pairtools/parse
pairtools/restrict
pairtools/select
pairtools/sort
pairtools/split
panacus/histgrowth
panacus/visualize
panaroo/run
pangolin/run
pangolin/updatedata
paraclu
paragraph/idxdepth
paragraph/multigrmpy
paragraph/vcf2paragraph
pasty
pbbam/pbmerge
pbccs
pbcpgtools/alignedbamtocpgscores
pbjasmine
pbmm2/align
pbptyper
pbsv/call
pbsv/discover
pbtk/bam2fastq
pbtk/pbindex
pbtk/pbmerge
peka
phantompeakqualtools
pharokka/installdatabases
pharokka/pharokka
phispy
phyloflash
picrust2/pipeline
pigz/uncompress
pindel/pindel
pints/caller
pirate
plasmidfinder
plasmidid
plastid/make_wiggle
plastid/metagene_generate
plastid/psite
plink2/extract
plink2/filter
plink2/het
plink2/indeppairwise
plink2/pca
plink2/remove
plink2/score
plink2/vcf
plink2/vcf2bgen
plink/bcf
plink/epistasis
plink/exclude
plink/extract
plink/fastepistasis
plink/genome
plink/gwas
plink/hwe
plink/indep
plink/indeppairwise
plink/ld
plink/recode
plink/vcf
plotsr
pmdtools/filter
pneumocat
polypolish/polish
poolsnp
popscle/demuxlet
popscle/dscpileup
popscle/freemuxlet
porechop/abi
porechop/porechop
portcullis/full
preseq/ccurve
president
presto/filterseq
prinseqplusplus
prodigal
prokka
proovframe/fix
proovframe/map
propr/grea
propr/logratio
propr/propd
propr/propr
proseg/proseg
proseg/proseg_to_baysor
proteinortho
proteus/readproteingroups
pureclip
purecn/coverage
purecn/intervalfile
purecn/normaldb
purecn/run
pychopper
pyclonevi
pycoqc
pydamage/analyze
pydamage/filter
pypgx/computecontrolstatistics
pypgx/createinputvcf
pypgx/preparedepthofcoverage
pypgx/runngspipeline
pyrodigal
qcat
qcatch
qualimap/bamqccram
quantmsutils/diann2mztab
quantmsutils/dianncfg
quantmsutils/mzmlstatistics
racon
rapidnj
rastair/call
rastair/mbias
rastair/mbiasparser
rastair/methylkit
raxmlng
regtools/junctionsextract
repeatmasker/repeatmasker
repeatmasker/rmouttogff3
repeatmodeler/builddatabase
repeatmodeler/repeatmodeler
resfinder/run
rgi/cardannotation
rgi/main
ribotish/predict
ribotish/quality
ribotricer/detectorfs
ribotricer/prepareorfs
ribowaltz
ripgrep
rmarkdownnotebook
rnaquast
roary
rrnatranscripts
rtn/tni
rundbcan/cazymeannotation
rundbcan/database
rundbcan/easycgc
rundbcan/easysubstrate
s4pred/runmodel
sageproteomics/sage
salsa2
sam2lca/analyze
sambamba/depth
sambamba/flagstat
sambamba/markdup
samblaster
sawfish/discover
scanpy/filter
scanpy/hashsolo
scanpy/pca
scanpy/scrublet
scds
scimap/mcmicro
scimap/spatiallda
scoary
scramble/clusteranalysis
scramble/clusteridentifier
scvitools/scar
scvitools/solo
seacr/callpeak
segemehl/align
segemehl/index
seqcluster/collapse
seqkit/concat
seqkit/fq2fa
seqkit/fx2tab
seqkit/head
seqkit/pair
seqkit/rmdup
seqkit/sana
seqkit/seq
seqkit/sliding
seqkit/sort
seqkit/split2
seqkit/tab2fx
seqkit/translate
seqsero2
sequali
sequencetools/pileupcaller
sequenzautils/bam2seqz
sequenzautils/gcwiggle
seqwish/induce
seroba/run
severus
sexdeterrmine
shasta
shasum
shigatyper
shigeifinder
shinyngs/app
shinyngs/staticdifferential
shinyngs/staticexploratory
shinyngs/validatefomcomponents
sickle
sigprofiler
simpleaf/index
simpleaf/quant
sistr
ska/distance
ska/fasta
skani/dist
skani/search
skani/sketch
skani/triangle
slamdunk/all
slamdunk/map
slimfastq
smoothxg
sniffles
snippy/core
snippy/run
snpdists
snpsift/annotate
snpsift/dbnsfp
snpsift/split
snpsites
souporcell
sourmash/compare
sourmash/gather
sourmash/index
sourmash/sketch
sourmash/taxannotate
sparsesignatures
spatyper
splitubam
spotiflow
srst2/srst2
ssuissero
stadeniolib/scramble
staphopiasccmec
staramr/search
stardist
stare
starfusion/build
starfusion/detect
star/starsolo
stecfinder
strdust
strelka/germline
strelka/somatic
stringtie/merge
summarizedexperiment/summarizedexperiment
svtyper/svtyper
svtyper/svtypersso
sylph/sketch
sylph/sketchgenomes
sylph/sketchsamples
sylphtax/merge
syri
tagbam
tailfindr
tar
taxonkit/lineage
taxonkit/list
taxonkit/name2taxid
taxpasta/merge
taxpasta/standardise
tbprofiler/profile
tcoffee/extractfrompdb
tcoffee/seqreformat
telseq
tesorter
tiara/tiara
tidk/explore
tidk/plot
tidk/search
tinc
topas/gencons
transdecoder/longorf
transdecoder/predict
trimal
trnascanse
trust4
trycycler/cluster
trycycler/subsample
tsebra
tximeta/tximport
ultra/align
ultra/index
ultra/pipeline
ultraplex
umitools/group
unicycler
universc
untarfiles
unzip
unzipfiles
vamb/bin
variancepartition/dream
variantbam
varscan/fpfilter
varscan/processsomatic
varscan/somatic
vcf2maf
vcf2zarr/convert
vcftools
vclust/align
vclust/cluster
vclust/prefilter
velocyto
verifybamid/verifybamid
vg/construct
vg/deconstruct
vg/index
viber
viennarna/rnacofold
viennarna/rnafold
viennarna/rnalfold
vireo
vizgenpostprocessing/compiletilesegmentation
vizgenpostprocessing/preparesegmentation
vizgenpostprocessing/runsegmentationontile
vrhyme/extractunbinned
vrhyme/linkbins
vrhyme/vrhyme
vt/decompose
vt/decomposeblocksub
vt/normalize
vuegen
wfmash
wget
wgsim
whamg
wipertools/fastqgather
wipertools/fastqscatter
wipertools/fastqwiper
wipertools/reportgather
xengsort/index
yak/count
yara/index
yara/mapper