# Authoritative nf-core module paths (generated by `catalog refresh-index`).
aardvark/compare
abacas
abra2
abricate/run
abricate/summary
abritamr/run
abyss/abysspe
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
alignoth
allelecounter
ampcombi
ampcombi2/cluster
ampcombi2/complete
ampcombi2/parsetables
ampir
amplify/predict
amps
amrfinderplus/run
amrfinderplus/update
amulety/antiberta2
amulety/antiberty
amulety/balmpaired
amulety/embed
amulety/esm2
amulety/translate
anarcii
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
any2fasta
apbs
arcashla/extract
argnorm
aria2
ariba/getref
ariba/run
arriba/arriba
arriba/download
arriba/visualisation
art/illumina
artic/aligntrim
artic/guppyplex
artic/minion
ascat
ashlar
assemblyscan
ataqv/ataqv
ataqv/mkarv
atlas/call
atlas/pmd
atlas/recal
atlas/splitmerge
atlasgeneannotationmanipulation/gtf2featureannotation
authentict/deam2cont
autocycler/cluster
autocycler/combine
autocycler/compress
autocycler/resolve
autocycler/subsample
autocycler/trim
backsub
bacphlip
bakta/bakta
bakta/baktadbdownload
bam2fastx/bam2fastq
bamaligncleaner
bamclipper
bamcmp
bamreadcount
bamstats/generalstats
bamtofastq10x
bamtools/convert
bamtools/split
bamtools/stats
bamutil/clipoverlap
bamutil/trimbam
bandage/image
barrnap
bases2fastq
basicpy
baysor/preview
baysor/run
baysor/segfree
bbmap/align
bbmap/bbduk
bbmap/bbmerge
bbmap/bbnorm
bbmap/bbsplit
bbmap/clumpify
bbmap/filterbyname
bbmap/index
bbmap/pileup
bbmap/repair
bbmap/sendsketch
bcftools/annotate
bcftools/call
bcftools/concat
bcftools/consensus
bcftools/convert
bcftools/csq
bcftools/filter
bcftools/index
bcftools/isec
bcftools/merge
bcftools/mpileup
bcftools/norm
bcftools/plotvcfstats
bcftools/pluginfilltags
bcftools/pluginfixploidy
bcftools/pluginimputeinfo
bcftools/pluginscatter
bcftools/pluginsetgt
bcftools/pluginsplit
bcftools/plugintag2tag
bcftools/pluginvcf2table
bcftools/query
bcftools/reheader
bcftools/roh
bcftools/rohviz
bcftools/sort
bcftools/split
bcftools/stats
bcftools/view
bcl2fastq
bclconvert
beagle5/beagle
bedgovcf
bedops/convert2bed
bedops/gtf2bed
bedtools/bamtobed
bedtools/closest
bedtools/complement
bedtools/coverage
bedtools/flank
bedtools/genomecov
bedtools/getfasta
bedtools/groupby
bedtools/intersect
bedtools/jaccard
bedtools/makewindows
bedtools/map
bedtools/maskfasta
bedtools/merge
bedtools/multiinter
bedtools/nuc
bedtools/shift
bedtools/shuffle
bedtools/slop
bedtools/sort
bedtools/split
bedtools/subtract
bedtools/unionbedg
bff
bftools/showinf
bigslice/bigslice
bigslice/downloaddb
bio2zarr/vcf2zarrconvert
bio2zarr/vcf2zarrexplode
bio2zarr/vcfpartition
bioawk
biobambam/bammarkduplicates2
biobambam/bammerge
biobambam/bamsormadup
bioformats2raw
biohansel
biomformat/convert
biscuit/align
biscuit/biscuitblaster
biscuit/bsconv
biscuit/epiread
biscuit/index
biscuit/mergecg
biscuit/pileup
biscuit/qc
biscuit/vcf2bed
bismark/align
bismark/coverage2cytosine
bismark/deduplicate
bismark/genomepreparation
bismark/methylationextractor
bismark/report
bismark/summary
blast/blastdbcmd
blast/blastn
blast/blastp
blast/makeblastdb
blast/tblastn
blast/updateblastdb
blat
blobtk/create
blobtk/depth
blobtk/plot
blobtk/snail
bowtie/align
bowtie/build
bowtie2/align
bowtie2/build
bracken/bracken
bracken/build
bracken/combinebrackenoutputs
braker3
busco/busco
busco/download
busco/generateplot
busco/phylogenomics
bwa/aln
bwa/index
bwa/mem
bwa/sampe
bwa/samse
bwafastalign/index
bwafastalign/mem
bwamem2/index
bwamem2/mem
bwamem3/index
bwamem3/mem
bwameme/index
bwameme/mem
bwameth/align
bwameth/index
caalm/caalm
caalm/downloadmodels
cadd
caddsv/get
cafe
calder2
canu
canvas/germline
carveme/carve
cat/cat
cat/fastq
catpack/addnames
catpack/bins
catpack/contigs
catpack/download
catpack/prepare
catpack/reads
catpack/summarise
cdhit/cdhit
cdhit/cdhitest
celesta
cellbender/merge
cellbender/removebackground
cellpose
cellranger/count
cellranger/mkfastq
cellranger/mkgtf
cellranger/mkref
cellranger/mkvdjref
cellranger/multi
cellranger/vdj
cellrangerarc/count
cellrangerarc/mkfastq
cellrangerarc/mkgtf
cellrangerarc/mkref
cellrangeratac/count
cellrangeratac/mkfastq
cellrangeratac/mkref
cellsnp/modea
centrifuge/build
centrifuge/centrifuge
centrifuge/kreport
centrifuger/build
centrifuger/centrifuger
centrifuger/quantification
checkm/lineagewf
checkm/qa
checkm2/databasedownload
checkm2/predict
checkqc
checkv/downloaddatabase
checkv/endtoend
checkv/updatedatabase
chelae/trim
chewbbaca/allelecall
chewbbaca/createschema
chopper
chromap/chromap
chromap/index
chromograph
circexplorer2/annotate
circexplorer2/parse
circularmapper/circulargenerator
circularmapper/realignsamfile
civicpy/annotate
clair3
clame
clipkit
clippy
clonalframeml
clustalo/align
clustalo/guidetree
clusty
cmaple
cmseq/polymut
cnaqc
cnvkit/access
cnvkit/antitarget
cnvkit/batch
cnvkit/call
cnvkit/coverage
cnvkit/export
cnvkit/fix
cnvkit/genemetrics
cnvkit/reference
cnvkit/segment
cnvkit/target
cnvnator/cnvnator
cnvnator/convert2vcf
cnvpytor/callcnvs
cnvpytor/histogram
cnvpytor/importreaddepth
cnvpytor/partition
cnvpytor/view
cobiontid/kmercounter
cobrameta
cobs/classicconstruct
cobs/compactconstruct
comebin/runcomebin
comet
concoct/concoct
concoct/concoctcoveragetable
concoct/cutupfasta
concoct/extractfastabins
concoct/mergecutupclustering
conifer
controlfreec/assesssignificance
controlfreec/freec
controlfreec/freec2bed
controlfreec/freec2circos
controlfreec/makegraph
controlfreec/makegraph2
cooler/balance
cooler/cload
cooler/digest
cooler/dump
cooler/makebins
cooler/merge
cooler/zoomify
cooltools/eigscis
cooltools/insulation
coptr/estimate
coptr/extract
coptr/index
coptr/map
coptr/merge
coreograph
coverm/contig
coverm/genome
cowpy
crabs/import
crabs/insilicopcr
crabz/compress
crabz/decompress
cramino
crisprcleanr/normalize
crispresso2
crumble
csvtk/concat
csvtk/join
csvtk/mutate2
csvtk/sort
csvtk/split
ctatsplicing/prepgenomelib
ctatsplicing/startocancerintrons
ctree
custom/addmostsevereconsequence
custom/addmostseverepli
custom/bed12codonpositions
custom/catadditionalfasta
custom/clustermetrics
custom/clustervisualization
custom/dumpsoftwareversions
custom/filterdifferentialtable
custom/geneticmapconvert
custom/getchromsizes
custom/gtffilter
custom/matrixfilter
custom/multiqccustombiotype
custom/orfcollapse
custom/orfmerge
custom/orfnormalise
custom/pcaclustering
custom/rsemmergecounts
custom/sratoolsncbisettings
custom/summarisetelomereestimation
custom/tabulartogseachip
custom/tabulartogseacls
custom/tabulartogseagct
custom/tx2gene
cutadapt
cutesv
damageprofiler
dastool/dastool
dastool/fastatocontig2bin
dastool/scaffolds2bin
datavzrd
deacon/filter
deacon/index
deacon/indexdiff
deacon/indexintersect
deacon/indexunion
decoupler/decoupler
dedup
deeparg/downloaddata
deeparg/predict
deepbgc/download
deepbgc/pipeline
deepcell/mesmer
deepmased/features
deepmased/predict
deepsomatic
deeptmhmm
deeptools/alignmentsieve
deeptools/bamcompare
deeptools/bamcoverage
deeptools/bigwigcompare
deeptools/computematrix
deeptools/multibamsummary
deeptools/multibigwigsummary
deeptools/plotcorrelation
deeptools/plotfingerprint
deeptools/plotheatmap
deeptools/plotpca
deeptools/plotprofile
deepvariant
deepvariant/callvariants
deepvariant/makeexamples
deepvariant/postprocessvariants
deepvariant/rundeepvariant
deepvariant/vcfstatsreport
delly/call
demuxem
deseq2/differential
diamond/blastp
diamond/blastx
diamond/cluster
diamond/deepclust
diamond/linclust
diamond/makedb
diann
diann/insilicolibrarygeneration
disambiguate
dotseq/dotseq
doubletdetection
dragen/germline
dragmap/align
dragmap/hashtable
dragonflye
drep/compare
drep/dereplicate
dshbio/exportsegments
dshbio/filterbed
dshbio/filtergff3
dshbio/splitbed
dshbio/splitgff3
dssp/mkdssp
dupblaster
duphold
dupradar
dysgu/run
ea-utils/gtf2bed
eagle2
eautils/fastqstats
echtvar/anno
echtvar/encode
ectyper
eggnogmapper
eido/convert
eido/validate
eigenstratdatabasetools/eigenstratsnpcoverage
eklipse
elprep/fastatoelfasta
elprep/filter
elprep/merge
elprep/split
emboss/cons
emboss/revseq
emboss/seqret
emmtyper
emu/abundance
endorspy
ensemblvep/download
ensemblvep/filtervep
ensemblvep/vep
entrezdirect/esearch
entrezdirect/esummary
entrezdirect/xtract
epang/place
epang/split
epic2/epic2
estsfs
evigene/tr2aacds
expansionhunter
expansionhunterdenovo/merge
expansionhunterdenovo/profile
fairy/coverage
fairy/sketch
falco
falint
famsa/align
famsa/guidetree
faqcs
fargene
fast2q
fastani
fastavalidator
fastawindows
fastcov
fastdup
fastk/fastk
fastk/histex
fastk/merge
fastme
fastp
fastplong
fastqc
fastqdl
fastqe
fastqscan
fastqscreen/buildfromindex
fastqscreen/fastqscreen
fastqutils/info
fasttree
fastx/collapser
fcs/fcsadaptor
fcs/fcsgx
fcsgx/cleangenome
fcsgx/fetchdb
fcsgx/rungx
ferrohgvs/normalize
ferrohgvs/parse
ffq
fgbio/callduplexconsensusreads
fgbio/callmolecularconsensusreads
fgbio/collectduplexseqmetrics
fgbio/copyumifromreadname
fgbio/fastqtobam
fgbio/filterconsensusreads
fgbio/groupreadsbyumi
fgbio/sortbam
fgbio/zipperbams
fgumi/clip
fgumi/codec
fgumi/correct
fgumi/dedup
fgumi/downsample
fgumi/duplex
fgumi/duplexmetrics
fgumi/extract
fgumi/fastq
fgumi/filter
fgumi/group
fgumi/merge
fgumi/simplex
fgumi/simplexmetrics
fgumi/sort
fgumi/zipper
fibertoolsrs/addnucleosomes
fibertoolsrs/extract
fibertoolsrs/predictm6a
filtlong
finaletoolkit/adjustwps
finaletoolkit/aggbw
finaletoolkit/delfi
finaletoolkit/endmotifs
finaletoolkit/fraglengthbins
finaletoolkit/mds
finaletoolkit/wps
find/concatenate
find/unpigz
flash
flye
foldcomp/compress
foldcomp/decompress
foldmason/createdb
foldmason/easymsa
foldmason/msa2lddtreport
foldseek/createdb
foldseek/easysearch
force/cube
force/tileextent
fq/generate
fq/lint
fq/subsample
fqtk
freebayes
freyja/boot
freyja/demix
freyja/update
freyja/variants
fungtion/downloadmodels
fungtion/fungtion
fusioncatcher/build
fusioncatcher/fusioncatcher
fusioninspector
fusionreport/detect
fusionreport/download
galah
gamma/gamma
gangstr
ganon/buildcustom
ganon/classify
ganon/report
ganon/table
gappa/examineassign
gappa/examinegraft
gappa/examineheattree
gapseq/doall
gapseq/draft
gapseq/fill
gapseq/find
gapseq/findtransport
gapseq/medium
gatk/indelrealigner
gatk/realignertargetcreator
gatk/unifiedgenotyper
gatk4/addorreplacereadgroups
gatk4/analyzecovariates
gatk4/annotateintervals
gatk4/applybqsr
gatk4/applyvqsr
gatk4/asereadcounter
gatk4/baserecalibrator
gatk4/bedtointervallist
gatk4/calculatecontamination
gatk4/calibratedragstrmodel
gatk4/cleansam
gatk4/cnnscorevariants
gatk4/collectreadcounts
gatk4/collectsvevidence
gatk4/combinegvcfs
gatk4/composestrtablefile
gatk4/concordance
gatk4/condensedepthevidence
gatk4/createreadcountpanelofnormals
gatk4/createsequencedictionary
gatk4/createsomaticpanelofnormals
gatk4/denoisereadcounts
gatk4/determinegermlinecontigploidy
gatk4/estimatelibrarycomplexity
gatk4/fastqtosam
gatk4/filterintervals
gatk4/filtermutectcalls
gatk4/filtervarianttranches
gatk4/gatherbqsrreports
gatk4/gatherpileupsummaries
gatk4/genomicsdbimport
gatk4/genotypegvcfs
gatk4/germlinecnvcaller
gatk4/getpileupsummaries
gatk4/haplotypecaller
gatk4/indexfeaturefile
gatk4/intervallisttobed
gatk4/intervallisttools
gatk4/learnreadorientationmodel
gatk4/leftalignandtrimvariants
gatk4/markduplicates
gatk4/mergebamalignment
gatk4/mergemutectstats
gatk4/mergevcfs
gatk4/modelsegments
gatk4/mutect2
gatk4/postprocessgermlinecnvcalls
gatk4/preprocessintervals
gatk4/printreads
gatk4/printsvevidence
gatk4/reblockgvcf
gatk4/revertsam
gatk4/samtofastq
gatk4/selectvariants
gatk4/shiftfasta
gatk4/sitedepthtobaf
gatk4/splitcram
gatk4/splitintervals
gatk4/splitncigarreads
gatk4/svannotate
gatk4/svcluster
gatk4/unmarkduplicates
gatk4/variantfiltration
gatk4/variantrecalibrator
gatk4/variantstotable
gatk4spark/applybqsr
gatk4spark/baserecalibrator
gatk4spark/markduplicates
gawk
gcta/addgrms
gcta/adjustgrm
gcta/bivariatereml
gcta/bivariateremlldms
gcta/calculateldscores
gcta/grmcutoff
gcta/keep
gcta/makebksparse
gcta/makegrm
gcta/makegrmpart
gcta/reml
gcta/remlldms
gecco/convert
gecco/run
gedi/indexgenome
gedi/price
gem2/gem2bedmappability
gem2/gemindexer
gem2/gemmappability
gem3/gem3indexer
gem3/gem3mapper
gemmi/cif2json
genescopefk
genin2
genmap/index
genmap/map
genmod/annotate
genmod/compound
genmod/models
genmod/score
genomad/download
genomad/endtoend
genomescope2
genotyphi/parse
genrich
gens/preparecovandbaf
geofetch
geoquery/getgeo
getorganelle/config
getorganelle/fromreads
gfaffix
gfastats
gfatools/gfa2fa
gfatools/stat
gffcompare
gffread
gget/gget
glimpse/chunk
glimpse/concordance
glimpse/ligate
glimpse/phase
glimpse/sample
glimpse2/chunk
glimpse2/concordance
glimpse2/ligate
glimpse2/phase
glimpse2/splitreference
glnexus
gmmdemux
gnu/sort
gnu/split
goat/taxonsearch
goatools/findenrichment
goleft/indexcov
goleft/indexsplit
gprofiler2/gost
grabix/check
graphmap2/align
graphmap2/index
graphtyper/genotype
graphtyper/vcfconcatenate
gridss/annotate
gridss/generateponbedpe
gridss/gridss
gridss/somaticfilter
grimer
gsea/gsea
gstama/collapse
gstama/merge
gstama/polyacleanup
gt/gff3
gt/gff3validator
gt/ltrharvest
gt/stat
gt/suffixerator
gtdbtk/classifywf
gtdbtk/gtdbtoncbimajorityvote
gtfsort
gubbins
gunc/downloaddb
gunc/mergecheckm
gunc/run
gunzip
gvcftools/extractvariants
gzrt
hamronization/abricate
hamronization/amrfinderplus
hamronization/deeparg
hamronization/fargene
hamronization/rgi
hamronization/summarize
hapibd
haplocheck
haplogrep2/classify
haplogrep3/classify
happy/ftxpy
happy/happy
happy/prepy
happy/sompy
hasheddrops
helitronscanner/draw
helitronscanner/scan
hhsuite/hhblits
hhsuite/hhsearch
hhsuite/reformat
hicap
hicexplorer/hicpca
hifiadapterfilt/downloaddb
hifiadapterfilt/hifiadapterfilt
hifiasm
hificnv
hifitrimmer/filterbam
hifitrimmer/processblast
hiphase
hisat2/align
hisat2/build
hisat2/extractsplicesites
hisat3n/align
hisat3n/build
hlala/preparegraph
hlala/typing
hmmcopy/gccounter
hmmcopy/generatemap
hmmcopy/mapcounter
hmmcopy/readcounter
hmmer/eslalimask
hmmer/eslalipid
hmmer/eslreformat
hmmer/hmmalign
hmmer/hmmbuild
hmmer/hmmemit
hmmer/hmmfetch
hmmer/hmmlogo
hmmer/hmmpress
hmmer/hmmrank
hmmer/hmmsearch
hmmer/hmmstat
hmmer/jackhmmer
hmtnote/annotate
holodeck/eval
holodeck/methylate
holodeck/mutate
holodeck/simulate
homer/annotatepeaks
homer/findpeaks
homer/maketagdirectory
homer/makeucscfile
homer/pos2bed
hostile/clean
hostile/fetch
hpsuissero
htodemux
htseq/count
htslib/bgziptabix
htsnimtools/vcfcheck
huggingface/download
humann3/humann
humann3/regroup
humann3/renorm
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
imc2mc
immunedeconv
infernal/cmsearch
instrain/compare
instrain/profile
integronfinder
interproscan
iphop/download
iphop/predict
iqtree
irescue
islandpath
ismapper
isoseq/cluster
isoseq/refine
isoseq3/tag
ivar/consensus
ivar/trim
ivar/variants
jasminesv
jellyfish/count
jellyfish/dump
juicertools/pre
jupyternotebook
jvarkit/dict2bed
jvarkit/sam2tsv
jvarkit/vcf2table
jvarkit/vcffilterjdk
jvarkit/vcfpolyx
jvarkit/wgscoverageplotter
kaiju/kaiju
kaiju/kaiju2krona
kaiju/kaiju2table
kaiju/mergeoutputs
kaiju/mkfmi
kalign/align
kallisto/index
kallisto/quant
kallistobustools/count
kallistobustools/ref
kat/hist
khmer/normalizebymedian
khmer/trimlowabund
khmer/uniquekmers
kleborate
kled
kma/index
kma/kma
kmcp/compute
kmcp/index
kmcp/merge
kmcp/profile
kmcp/search
kmergenie
knotannotsv
kofamscan
kraken2/add
kraken2/build
kraken2/buildstandard
kraken2/kraken2
krakentools/combinekreports
krakentools/extractkrakenreads
krakentools/kreport2krona
krakenuniq/build
krakenuniq/download
krakenuniq/preloadedkrakenuniq
krona/kronadb
krona/ktimportkrona
krona/ktimporttaxonomy
krona/ktimporttext
krona/ktupdatetaxonomy
last/dotplot
last/lastal
last/lastdb
last/mafconvert
last/mafswap
last/postmask
last/split
last/train
leafcutter/clusterregtools
learnmsa/align
leehom
legsta
leviosam2/index
leviosam2/lift
liftoff
lima
limma/differential
links
lissero
llamacpppython/run
localcdsearch/annotate
localcdsearch/download
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
macse/refinealignment
macsyfinder/download
macsyfinder/search
mafft/align
mafft/guidetree
mageck/count
mageck/mle
mageck/test
magus/align
magus/guidetree
mako
malt/build
malt/run
maltextract
manta/convertinversion
manta/germline
manta/somatic
manta/tumoronly
mapad/index
mapad/map
mapdamage2
mash/dist
mash/screen
mash/sketch
mashmap
mashtree
mat2json
maxbin2
maxquant/lfq
mcquant
mcroni
mcstaging/imc2mc
mcstaging/macsima2mc
mcstaging/phenoimager2mc
md5sum
mdust
medaka
megahit
megan/daa2info
megan/rma2info
melon
memote/report
memote/run
meningotype
merfin/hist
merqury/hapmers
merqury/merqury
merquryfk/hapmaker
merquryfk/katcomp
merquryfk/katgc
merquryfk/merquryfk
merquryfk/ploidyplot
meryl/count
meryl/histogram
meryl/unionsum
metabat2/jgisummarizebamcontigdepths
metabat2/metabat2
metabuli/build
metacache/build
metacache/query
metaeuk/easypredict
metamaps/classify
metamaps/mapdirectly
metamdbg/asm
metaphlan/makedb
metaphlan/mergemetaphlantables
metaphlan/metaphlan
metaphlan3/mergemetaphlantables
metaphlan3/metaphlan3
metaspace/converter
metaspace/download
metator/pipeline
methbat/profile
methurator/gtestimator
methurator/plot
methyldackel/extract
methyldackel/mbias
methylsieve
mgikit/demultiplex
midas/run
mifaser
mindagap/duplicatefinder
mindagap/mindagap
minia
miniasm
minibwa/index
minibwa/map
minimac4/compressref
minimac4/impute
minimap2/align
minimap2/index
miniprot/align
miniprot/index
miranda
mirdeep2/mapper
mirdeep2/mirdeep2
mirtop/counts
mirtop/export
mirtop/gff
mirtop/stats
mirtrace/qc
misopy/index
mitohifi/findmitoreference
mitohifi/mitohifi
mitorsaw/haplotype
mlst
mmseqs/cluster
mmseqs/createdb
mmseqs/createindex
mmseqs/createtaxdb
mmseqs/createtsv
mmseqs/databases
mmseqs/easycluster
mmseqs/easysearch
mmseqs/linclust
mmseqs/makepaddedseqdb
mmseqs/search
mmseqs/taxonomy
mmseqs/tsv2exprofiledb
mobster
mobsuite/recon
modkit/bedmethyltobigwig
modkit/callmods
modkit/pileup
modkit/repair
molkartgarage/clahe
mosdepth
motus/downloaddb
motus/merge
motus/preplong
motus/profile
msisensor/msi
msisensor/scan
msisensor2/msi
msisensorpro/msisomatic
msisensorpro/pro
msisensorpro/scan
mtmalign/align
mtnucratio
mudskipper/bulk
mudskipper/index
multiqc
multiqcsav
multiseqdemux
multivcfanalyzer
mummer
muscle
muscle5/super5
muse/call
muse/sump
mygene
mykrobe/predict
myloasm
nacho/normalize
nacho/qc
nail/search
nanocomp
nanofilt
nanolyse
nanomonsv/get
nanomonsv/parse
nanoplot
nanoq
narfmap/align
narfmap/hashtable
ncbigenomedownload
ncbitools/vecscreen
nextclade/datasetget
nextclade/run
nextgenmap
ngmaster
ngmerge
ngsbits/bedannotategc
ngsbits/bedcoverage
ngsbits/rohhunter
ngsbits/samplegender
ngsbits/updhunter
ngscheckmate/fastq
ngscheckmate/ncm
ngscheckmate/patterngenerator
ngscheckmate/vafncm
nonpareil/curve
nonpareil/nonpareil
nonpareil/nonpareilcurvesr
nonpareil/set
nucmer
numorph/3dunet
numorph/intensity
numorph/resample
oatk
octopusv/clean
octopusv/correct
octopusv/merge
octopusv/plot
octopusv/stat
octopusv/svcf2vcf
odgi/build
odgi/draw
odgi/layout
odgi/sort
odgi/squeeze
odgi/stats
odgi/unchop
odgi/view
odgi/viz
oncocnv
openms/decoydatabase
openms/fileconverter
openms/filefilter
openms/idfilter
openms/idmassaccuracy
openms/idmerger
openms/idripper
openms/idscoreswitcher
openms/peakpickerhires
openms/peptideindexer
openms/psmfeatureextractor
openms/textexporter
openmsthirdparty/cometadapter
opt/flip
opt/stat
opt/track
optitype
orfipy
orthofinder
osfclient/fetch
paftools/sam2paf
pairix
pairtools/dedup
pairtools/flip
pairtools/merge
pairtools/parse
pairtools/restrict
pairtools/select
pairtools/sort
pairtools/split
pairtools/stats
panacus/histgrowth
panacus/visualize
panaroo/run
pangolin/run
pangolin/updatedata
parabricks/applybqsr
parabricks/dbsnp
parabricks/deepvariant
parabricks/fq2bam
parabricks/fq2bammeth
parabricks/genotypegvcf
parabricks/haplotypecaller
parabricks/indexgvcf
parabricks/minimap2
parabricks/mutectcaller
parabricks/rnafq2bam
parabricks/starfusion
paraclu
paragraph/idxdepth
paragraph/multigrmpy
paragraph/vcf2paragraph
paraphase
paraphrase
parsesdrf/convert
parsnp
pasty
pbbam/pbmerge
pbccs
pbcpgtools/alignedbamtocpgscores
pbjasmine
pbmarkdup
pbmm2/align
pbptyper
pbsv/call
pbsv/discover
pbtk/bam2fastq
pbtk/pbindex
pbtk/pbmerge
pcgr/getref
pcne
pdb2pqr
pear
peddy
peka
perbase
percolator
phantompeakqualtools
pharmcat/matcher
pharmcat/phenotyper
pharmcat/reporter
pharmcat/vcfpreprocessor
pharokka/installdatabases
pharokka/pharokka
phenoimager2mc
phispy
phyloflash
picard/addorreplacereadgroups
picard/bedtointervallist
picard/cleansam
picard/collectalignmentsummarymetrics
picard/collecthsmetrics
picard/collectinsertsizemetrics
picard/collectmultiplemetrics
picard/collectrnaseqmetrics
picard/collectvariantcallingmetrics
picard/collectwgsmetrics
picard/createsequencedictionary
picard/crosscheckfingerprints
picard/extractfingerprint
picard/fastqtosam
picard/filtersamreads
picard/fixmateinformation
picard/liftovervcf
picard/markduplicates
picard/meanqualitybycycle
picard/mergesamfiles
picard/positionbaseddownsamplesam
picard/renamesampleinvcf
picard/scatterintervalsbyns
picard/setnmmdanduqtags
picard/sortsam
picard/sortvcf
picard/splitsambynumberofreads
picrust2/pipeline
pigz/compress
pigz/uncompress
pilon
pindel/pindel
pints/caller
pirate
plasmidfinder
plasmidid
plastid/make_wiggle
plastid/metagene_generate
plastid/psite
platypus
plink/bcf
plink/epistasis
plink/exclude
plink/extract
plink/fastepistasis
plink/genome
plink/gwas
plink/hwe
plink/indep
plink/indeppairwise
plink/ld
plink/missing
plink/recode
plink/vcf
plink2/extract
plink2/filter
plink2/het
plink2/indeppairwise
plink2/pca
plink2/pmerge
plink2/remove
plink2/score
plink2/vcf
plink2/vcf2bgen
plotsr
pmdtools/filter
pneumocat
polypolish/polish
poolsnp
popscle/demuxlet
popscle/dscpileup
popscle/freemuxlet
porechop/abi
porechop/porechop
portcullis/full
portello
preseq/ccurve
preseq/lcextrap
president
presto/filterseq
pretextmap
pretextsnapshot
pridepy/downloadfile
pridepy/fetchsdrf
primerprospector/analyzeprimers
prinseqplusplus
prodigal
prokka
proovframe/fix
proovframe/map
propr/grea
propr/logratio
propr/propd
propr/propr
proseg/proseg
proseg/proseg2baysor
proteinortho
proteus/readproteingroups
pureclip
purecn/coverage
purecn/intervalfile
purecn/normaldb
purecn/run
purgedups/calcuts
purgedups/getseqs
purgedups/histplot
purgedups/pbcstat
purgedups/purgedups
purgedups/splitfa
pychopper
pyclonevi
pycoqc
pydamage/analyze
pydamage/filter
pygenprop/build
pygenprop/info
pypgx/computecontrolstatistics
pypgx/createinputvcf
pypgx/preparedepthofcoverage
pypgx/runngspipeline
pypolca/run
pyrodigal
qcat
qcatch
qsv/cat
qualimap/bamqc
qualimap/bamqccram
qualimap/rnaseq
quantmsutils/diann2mztab
quantmsutils/dianncfg
quantmsutils/mzmlstatistics
quartonotebook
quast
quilt/quilt
quilt/quilt2
racon
ragtag/patch
ragtag/scaffold
rapidnj
rastair/call
rastair/mbias
rastair/mbiasparser
rastair/methylkit
rasusa
rattle/cluster
raven
raw2ometiff
raxmlng
rbt/vcfsplit
refsolver/compare
refsolver/identify
refsolver/score
regenie/runl0
regenie/splitl0
regenie/step1
regenie/step2
regtools/junctionsextract
repeatmasker/repeatmasker
repeatmasker/rmouttogff3
repeatmodeler/builddatabase
repeatmodeler/repeatmodeler
resfinder/run
rgi/bwt
rgi/cardannotation
rgi/main
rhocall/annotate
rhocall/viz
ribocode/gtfupdate
ribocode/metaplots
ribocode/prepare
ribocode/ribocode
ribodetector
ribotish/predict
ribotish/quality
ribotricer/detectorfs
ribotricer/prepareorfs
ribowaltz
riker/multi
ripgrep
rmarkdownnotebook
rmats/prep
rnaquast
roary
rpbp/estimatemetagenebayesfactors
rpbp/estimateorfbayesfactors
rpbp/extractmetageneprofiles
rpbp/extractorfprofiles
rpbp/getperiodiclengthsoffsets
rpbp/preparegenome
rpbp/selectfinalpredictionset
rpbp/selectperiodicoffsets
rrnatranscripts
rsem/calculateexpression
rsem/preparereference
rseqc/bamstat
rseqc/inferexperiment
rseqc/innerdistance
rseqc/junctionannotation
rseqc/junctionsaturation
rseqc/readdistribution
rseqc/readduplication
rseqc/splitbam
rseqc/tin
rtgtools/bndeval
rtgtools/cnveval
rtgtools/format
rtgtools/pedfilter
rtgtools/rocplot
rtgtools/svdecompose
rtgtools/vcfeval
rtn/tni
rundbcan/cazymeannotation
rundbcan/database
rundbcan/easycgc
rundbcan/easysubstrate
rustqc
s4pred/runmodel
sageproteomics/sage
salmon/index
salmon/quant
salsa2
saltshaker/call
saltshaker/classify
saltshaker/plot
sam2lca/analyze
sambamba/depth
sambamba/flagstat
sambamba/markdup
samblaster
samclip
samplesheetparser/diff
samplesheetparser/info
samplesheetparser/validate
samshee
samtools/addreplacerg
samtools/ampliconclip
samtools/bam2fq
samtools/bedcov
samtools/bgzip
samtools/calmd
samtools/cat
samtools/collate
samtools/collatefastq
samtools/consensus
samtools/convert
samtools/coverage
samtools/cramsize
samtools/depth
samtools/dict
samtools/faidx
samtools/fasta
samtools/fastq
samtools/fixmate
samtools/flagstat
samtools/getrg
samtools/idxstats
samtools/import
samtools/index
samtools/markdup
samtools/merge
samtools/mpileup
samtools/quickcheck
samtools/reheader
samtools/samples
samtools/sormadup
samtools/sort
samtools/splitheader
samtools/stats
samtools/view
savana/classify
savana/cna
savana/run
sawfish/discover
sawfish/jointcall
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
segul/aligntrim
semibin/singleeasybin
sentieon/applyvarcal
sentieon/bwaindex
sentieon/bwamem
sentieon/collectvcmetrics
sentieon/coveragemetrics
sentieon/datametrics
sentieon/dedup
sentieon/dnamodelapply
sentieon/dnascope
sentieon/gvcftyper
sentieon/haplotyper
sentieon/hsmetrics
sentieon/qualcal
sentieon/readwriter
sentieon/rsemcalculateexpression
sentieon/rsempreparereference
sentieon/staralign
sentieon/tnfilter
sentieon/tnhaplotyper2
sentieon/tnscope
sentieon/varcal
sentieon/wgsmetrics
seq2hla
seqcluster/collapse
seqfu/check
seqfu/derep
seqfu/stats
seqkit/concat
seqkit/fq2fa
seqkit/fx2tab
seqkit/grep
seqkit/head
seqkit/pair
seqkit/replace
seqkit/rmdup
seqkit/sample
seqkit/sana
seqkit/seq
seqkit/sliding
seqkit/sort
seqkit/split2
seqkit/stats
seqkit/tab2fx
seqkit/translate
seqsero2
seqtk/comp
seqtk/cutn
seqtk/mergepe
seqtk/rename
seqtk/sample
seqtk/seq
seqtk/subseq
seqtk/trim
sequali
sequencetools/pileupcaller
sequenzautils/bam2seqz
sequenzautils/gcwiggle
seqwish/induce
seroba/run
severus
sexdeterrmine
sgdemux
shapeit5/ligate
shapeit5/phasecommon
shapeit5/phaserare
shapeit5/switch
shasta
shasum
shigapass
shigatyper
shigeifinder
shinyngs/app
shinyngs/staticdifferential
shinyngs/staticexploratory
shinyngs/validatefomcomponents
shovill
sickle
sigprofiler
simpleaf/index
simpleaf/quant
singlem/dbdownload
sistr
ska/distance
ska/fasta
skani/dist
skani/search
skani/sketch
skani/triangle
skesa
slamdunk/all
slamdunk/map
slimfastq
smncopynumbercaller
smoothxg
smoove/call
snakemake
snapaligner/align
snapaligner/index
sniffles
snippy/core
snippy/run
snpdists
snpeff/download
snpeff/snpeff
snpsift/annmem
snpsift/annmemcreate
snpsift/annotate
snpsift/dbnsfp
snpsift/split
snpsites
somalier/ancestry
somalier/extract
somalier/relate
sortmerna
souporcell
soupx
sourcepredict
sourmash/compare
sourmash/gather
sourmash/index
sourmash/sketch
sourmash/taxannotate
spaceranger/count
spaceranger/mkgtf
spaceranger/mkref
spades
sparsesignatures
spatyper
splitubam
spotiflow
spring/compress
spring/decompress
sratools/fasterqdump
sratools/prefetch
srst2/srst2
ssuissero
stacks/refmap
stadeniolib/scramble
stainwarpy/extractchannel
stainwarpy/register
stainwarpy/transformsegmask
staphopiasccmec
staphscan
star/align
star/genomegenerate
star/indexversion
star/starsolo
staramr/search
stardist
stare
starfusion/build
starfusion/detect
stecfinder
stitch
stranger
strdrop/build
strdrop/call
strdust
strelka/germline
strelka/somatic
stringtie/merge
stringtie/stringtie
strobealign
strvctvre/strvctvre
subread/featurecounts
summarizedexperiment/summarizedexperiment
survivor/bedpetovcf
survivor/filter
survivor/merge
survivor/simsv
survivor/stats
sushie
svaba
svanalyzer/svbenchmark
svdb/build
svdb/merge
svdb/query
svdss/index
svim/alignment
svtk/baftest
svtk/countsvtypes
svtk/rdtest2vcf
svtk/standardize
svtk/vcf2bed
svtools/vcftobedpe
svtyper/svtyper
svtyper/svtypersso
svync
sylph/profile
sylph/sketch
sylph/sketchgenomes
sylph/sketchsamples
sylphtax/merge
sylphtax/taxprof
syri
t1k/build
t1k/run
tabix/bgzip
tabix/bgziptabix
tabix/tabix
tagbam
tailfindr
tar
taxonkit/lineage
taxonkit/list
taxonkit/name2taxid
taxpasta/merge
taxpasta/standardise
tbprofiler/profile
tcoffee/align
tcoffee/alncompare
tcoffee/consensus
tcoffee/extractfrompdb
tcoffee/irmsd
tcoffee/regressive
tcoffee/seqreformat
tcoffee/tcs
td2/longorfs
td2/predict
telescope/assign
telogator2
telomerehunter
telseq
tesorter
tetranscripts
thermorawfileparser
tiara/tiara
tiddit/cov
tiddit/sv
tidk/explore
tidk/plot
tidk/search
tinc
tmb/pytmb
topas/gencons
toulligqc
traitar/pfamget
traitar/run
transdecoder/longorf
transdecoder/predict
trgt/genotype
trgt/merge
trgt/plot
trimal
trimgalore
trimmomatic
trinity
trnascanse
trtools/dumpstr
trtools/mergestr
trust4
truvari/bench
truvari/consistency
truvari/segment
trycycler/cluster
trycycler/subsample
tsebra
tximeta/tximport
ucsc/bedclip
ucsc/bedgraphtobigwig
ucsc/bedtobigbed
ucsc/bigwigaverageoverbed
ucsc/gtftogenepred
ucsc/liftover
ucsc/wigtobigwig
ultra/align
ultra/index
ultra/pipeline
ultraplex
umicollapse
umitools/dedup
umitools/extract
umitools/group
umitools/prepareforrsem
unicycler
universc
untar
untarfiles
unzip
unzipfiles
upd
upp/align
vamb/bin
vardictjava
variancepartition/dream
variantbam
variantextractor
varlociraptor/callvariants
varlociraptor/estimatealignmentproperties
varlociraptor/filterfdr
varlociraptor/preprocess
varscan/fpfilter
varscan/processsomatic
varscan/somatic
vcf2cytosure
vcf2db
vcf2maf
vcf2zarr/convert
vcf2zarr/explode
vcfanno
vcfexpress
vcflib/vcfbreakmulti
vcflib/vcffilter
vcflib/vcffixup
vcflib/vcfuniq
vcfpgloader/load
vcftools
vclust/align
vclust/cluster
vclust/prefilter
velocyto
vembrane/filter
vembrane/sort
vembrane/table
verifybamid/verifybamid
verifybamid/verifybamid2
vg/construct
vg/deconstruct
vg/index
viber
viennarna/rnacofold
viennarna/rnafold
viennarna/rnalfold
viralconsensus
vireo
virusrecom
vizgenpostprocessing/compiletilesegmentation
vizgenpostprocessing/preparesegmentation
vizgenpostprocessing/runsegmentationontile
vrhyme/extractunbinned
vrhyme/linkbins
vrhyme/vrhyme
vsearch/cluster
vsearch/dereplicate
vsearch/fastqfilter
vsearch/sintax
vsearch/sort
vsearch/usearchglobal
vt/decompose
vt/decomposeblocksub
vt/normalize
vuegen
wfmash
wget
wgsim
whamg
whatshap/haplotag
whatshap/phase
whatshap/stats
windowmasker/convert
windowmasker/mkcounts
windowmasker/ustat
wipertools/fastqgather
wipertools/fastqscatter
wipertools/fastqwiper
wipertools/reportgather
wisecondorx/convert
wisecondorx/gender
wisecondorx/newref
wisecondorx/predict
wittyer
xengsort/index
xeniumranger/import-segmentation
xeniumranger/relabel
xeniumranger/rename
xeniumranger/resegment
xz/compress
xz/decompress
yahs
yak/count
yara/index
yara/mapper
yte
zip

# --- catalog-local (preserved across refresh) ---
qiime2/ancombc
qiime2/barplot
qiime2/diversityalphararefaction
qiime2/diversitycore
qiime2/relativeabundancetables
rtgtools/vcfeval
happy/happy
happy/sompy
truvari/bench
svanalyzer/svbenchmark
wittyer
