Skip to content
Logo LogoSnakemake wrappers
Homepage Plugin catalog Workflow catalog
⌘ K
Logo LogoSnakemake wrappers
Homepage Plugin catalog Workflow catalog

Wrappers and Meta-Wrappers

  • Wrappers
    • ADAPTERREMOVAL
    • ARRIBA
    • ART
      • ART_PROFILER_ILLUMINA
    • ASSEMBLY-STATS
    • BAMTOOLS
      • BAMTOOLS FILTER
      • BAMTOOLS FILTER WITH JSON
      • BAMTOOLS SPLIT
      • BAMTOOLS STATS
    • BARRNAP
    • BAZAM
    • BBMAP-SUITE
    • BCFTOOLS
      • BCFTOOLS CALL
      • BCFTOOLS CONCAT
      • BCFTOOLS FILTER
      • BCFTOOLS INDEX
      • BCFTOOLS MERGE
      • BCFTOOLS MPILEUP
      • BCFTOOLS NORM
      • BCFTOOLS REHEADER
      • BCFTOOLS SORT
      • BCFTOOLS STATS
      • BCFTOOLS VIEW
    • BEDTOOLS
      • BAMTOBED
      • COMPLEMENTBED
      • COVERAGEBED
      • GENOMECOVERAGEBED
      • INTERSECTBED
      • MERGEBED
      • SLOPBED
      • SORTBED
      • BEDTOOLS SPLIT
    • BELLEROPHON
    • BENCHMARK
      • CHM-EVAL
      • CHM-EVAL-KIT
      • CHM-EVAL-SAMPLE
    • BGZIP
    • BIOBAMBAM2
      • BIOBAMBAM2 BAMSORMADUP
    • BISMARK
      • BAM2NUC
      • BISMARK
      • BISMARK2BEDGRAPH
      • BISMARK2REPORT
      • BISMARK2SUMMARY
      • BISMARK_GENOME_PREPARATION
      • BISMARK_METHYLATION_EXTRACTOR
      • DEDUPLICATE_BISMARK
    • BLAST
      • BLAST BLASTN
      • BLAST MAKEBLASTDB FOR FASTA FILES
    • BOWTIE2
      • BOWTIE2
      • BOWTIE2_BUILD
    • BUSCO
    • BUSTOOLS
      • BUSTOOLS COUNT
      • BUSTOOLS SORT
      • BUSTOOLS TEXT
    • BWA
      • BWA ALN
      • BWA INDEX
      • BWA MEM
      • BWA MEM SAMBLASTER
      • BWA SAMPE
      • BWA SAMSE
      • BWA SAM(SE/PE)
    • BWA-MEM2
      • BWA-MEM2 INDEX
      • BWA-MEM2
      • BWA MEM SAMBLASTER
    • BWA-MEME
      • BWA-MEM2 INDEX
      • BWA-MEME
    • BWA-MEMX
      • BWA-MEM2 INDEX
      • BWA-MEMX
    • CAIROSVG
    • CLUSTALO
    • CNV_FACETS
    • CNVKIT
      • CNVKIT ANTITARGET
      • CNVKIT BATCH
      • CNVKIT CALL
      • CNVKIT DIAGRAM
      • CNVKIT EXPORT
      • CNVKIT TARGET
    • COOLPUP.PY
    • COOLTOOLS
      • COOLTOOLS DOTS
      • COOLTOOLS EIGS_CIS
      • COOLTOOLS EIGS_TRANS
      • COOLTOOLS EXPECTED_CIS
      • COOLTOOLS EXPECTED_TRANS
      • COOLTOOLS GENOME_BINNIFY
      • COOLTOOLS GENOME_GC
      • COOLTOOLS INSULATION
      • COOLTOOLS PILEUP
      • COOLTOOLS SADDLE
    • CSVTK
    • CUTADAPT
      • CUTADAPT-PE
      • CUTADAPT-SE
    • DADA2
      • DADA2_ADD_SPECIES
      • DADA2_ASSIGN_SPECIES
      • DADA2_ASSIGN_TAXONOMY
      • DADA2_COLLAPSE_NOMISMATCH
      • DADA2_DEREPLICATE_FASTQ
      • DADA2_FILTER_TRIM
      • DADA2_LEARN_ERRORS
      • DADA2_MAKE_TABLE
      • DADA2_MERGE_PAIRS
      • DADA2_QUALITY_PROFILES
      • DADA2_REMOVE_CHIMERAS
      • DADA2_SAMPLE_INFERENCE
    • DATAVZRD
    • DEEPTOOLS
      • DEEPTOOLS ALIGNMENT-SIEVE
      • DEEPTOOLS BAMCOVERAGE
      • DEEPTOOLS COMPUTEMATRIX
      • DEEPTOOLS PLOTCOVERAGE
      • DEEPTOOLS PLOTFINGERPRINT
      • DEEPTOOLS PLOTHEATMAP
      • DEEPTOOLS PLOTPROFILE
    • DEEPVARIANT
    • DELLY
    • DESEQ2
      • DESEQDATASET
      • DESEQ2
    • DIAMOND
      • DIAMOND BLASTP
      • DIAMOND BLASTX
      • DIAMOND MAKEDB
    • DRAGMAP
      • DRAGMAP
      • DRAGMAP
    • EGA
      • EGA FETCH
    • ENCODE_FASTQ_DOWNLOADER
    • ENHANCED VOLCANO
    • ENTREZ
      • EFETCH
    • EPIC
      • EPIC
    • FASTP
    • FASTQ_SCREEN
    • FASTQC
    • FASTTREE
    • FGBIO
      • FGBIO ANNOTATEBAMWITHUMIS
      • FGBIO CALLMOLECULARCONSENSUSREADS
      • FGBIO COLLECTDUPLEXSEQMETRICS
      • FGBIO FILTERCONSENSUSREADS
      • FGBIO GROUPREADSBYUMI
      • FGBIO SETMATEINFORMATION
    • FILTLONG
    • FREEBAYES
    • GALAH
    • GATK
      • GATK APPLYBQSR
      • GATK APPLYBQSRSPARK
      • GATK APPLYVQSR
      • GATK BASERECALIBRATOR
      • GATK BASERECALIBRATORSPARK
      • GATK CALCULATECONTAMINATION
      • GATK CALLCOPYRATIONSEGMENTS
      • GATK CLEANSAM
      • GATK COLLECTALLELICCOUNTS
      • GATK COLLECTREADCOUNTS
      • GATK COMBINEGVCFS
      • GATK DENOISEREADCOUNTS
      • GATK DEPTHOFCOVERAGE
      • GATK ESTIMATELIBRARYCOMPLEXITY
      • GATK FILTERMUTECTCALLS
      • GATK GENOMICSDBIMPORT
      • GATK GENOTYPEGVCFS
      • GATK GETPILEUPSUMMARIES
      • GATK HAPLOTYPECALLER
      • GATK INTERVALLISTTOBED
      • GATK LEARNREADORIENTATIONMODEL
      • GATK LEFTALIGNANDTRIMVARIANTS
      • GATK MARKDUPLICATESSPARK
      • GATK MODELSEGMENTS
      • GATK MUTECT2
      • GATK PRINTREADSSPARK
      • GATK SCATTERINTERVALSBYNS
      • GATK SELECTVARIANTS
      • GATK SPLITINTERVALS
      • GATK SPLITNCIGARREADS
      • GATK VARIANTANNOTATOR
      • GATK VARIANTEVAL
      • GATK VARIANTFILTRATION
      • GATK VARIANTRECALIBRATOR
      • GATK VARIANTSTOTABLE
    • GATK3
      • GATK3 BASERECALIBRATOR
      • GATK3 INDELREALIGNER
      • GATK3 PRINTREADS
      • GATK3 REALIGNERTARGETCREATOR
    • GDC-API
      • GDC API-BASED DATA DOWNLOAD OF BAM SLICES
    • GDC-CLIENT
      • GDC DATA TRANSFER TOOL DATA DOWNLOAD
    • GENEFUSE
    • GENOMEPY
    • GENOMESCOPE
    • GFATOOLS
    • GFFREAD
    • GRIDSS
      • GRIDSS ASSEMBLE
      • GRIDSS CALL
      • GRIDSS PREPROCESS
      • GRIDSS SETUPREFERENCE
    • GSEAPY
      • GSEAPY GSEA
    • HAP.PY
      • HAP.PY
      • PRE.PY
    • HIFIASM
    • HISAT2
      • HISAT2 ALIGN
      • HISAT2 INDEX
    • HMMER
      • HMMBUILD
      • HMMPRESS
      • HMMSCAN
      • HMMSEARCH
    • HOMER
      • HOMER ANNOTATEPEAKS
      • HOMER FINDPEAKS
      • HOMER GETDIFFERENTIALPEAKS
      • HOMER MAKETAGDIRECTORY
      • HOMER MERGEPEAKS
    • IGV-REPORTS
    • IMMUNEDECONV
    • INFERNAL
      • INFERNAL CMPRESS
      • INFERNAL CMSCAN
    • JANNOVAR
    • JELLYFISH
      • JELLYFISH_COUNT
      • JELLYFISH_DUMP
      • JELLYFISH_HISTO
      • JELLYFISH_MERGE
    • KALLISTO
      • KALLISTO INDEX
      • KALLISTO QUANT
    • LAST
      • LASTAL
      • LASTDB
    • LIFTOFF
    • LOFREQ
      • LOFREQ CALL
      • LOFREQ INDELQUAL
    • MACS2
      • MACS2 CALLPEAK
    • MANTA
    • MAPDAMAGE2
    • MASHMAP
    • MERQURY
    • MERYL
      • MERYL COUNT
      • MERYL SETS
      • MERYL STATS
    • METHYLDACKEL
      • METHYLDACKEL EXTRACT
    • MICROPHASER
      • MICROPHASER BUILD_REFERENCE
      • MICROPHASER FILTER
      • MICROPHASER NORMAL
      • MICROPHASER SOMATIC
    • MINIMAP2
      • MINIMAP2
      • MINIMAP2 INDEX
    • MLST
    • MOSDEPTH
    • MSISENSOR
      • MSISENSOR MSI
      • MSISENSOR SCAN
    • MULTIQC
    • MUSCLE
    • NANOSIM-H
    • NEXTFLOW
    • NGS-DISAMBIGUATE
    • NONPAREIL
      • NONPAREIL INFER
      • NONPAREIL PLOT
    • OPEN-CRAVAT
      • OPENCRAVAT MODULE
      • OPENCRAVAT RUN
    • OPTITYPE
    • PALADIN
      • PALADIN ALIGN
      • PALADIN INDEX
      • PALADIN PREPARE
    • PANDORA
      • PANDORA INDEX
    • PBMM2
      • PBMM2 ALIGN
      • PBMM2 INDEX
    • PEAR
    • PICARD
      • PICARD ADDORREPLACEREADGROUPS
      • PICARD BEDTOINTERVALLIST
      • PICARD COLLECTALIGNMENTSUMMARYMETRICS
      • PICARD COLLECTGCBIASMETRICS
      • PICARD COLLECTHSMETRICS
      • PICARD COLLECTINSERTSIZEMETRICS
      • PICARD COLLECTMULTIPLEMETRICS
      • PICARD COLLECTRNASEQMETRICS
      • PICARD COLLECTTARGETEDPCRMETRICS
      • PICARD CREATESEQUENCEDICTIONARY
      • PICARD MARKDUPLICATES
      • PICARD MERGESAMFILES
      • PICARD MERGEVCFS
      • PICARD REVERTSAM
      • PICARD SAMTOFASTQ
      • PICARD SORTSAM
    • PINDEL
      • PINDEL
      • PINDEL2VCF
    • PLASS
    • PRESEQ
      • PRESEQ LC_EXTRAP
    • PRETEXT
      • PRETEXT MAP
      • PRETEXT MAP
      • PRETEXT MAP
    • PRIMERCLIP
    • PROSOLO
      • PROSOLO FDR CONTROL
      • PROSOLO
    • PTRIMMER
    • PURGE_DUPS
      • PURGE_DUPS CALCUTS
      • PURGE_DUPS GET_SEQS
      • PURGE_DUPS NGSCSTAT
      • PURGE_DUPS PBCSTAT
      • PURGE_DUPS
      • PURGE_DUPS SPLIT_FA
    • PYFASTAQ
      • PYFASTAQ REPLACE_BASES
    • PYROE
      • PYROE ID-TO-NAME
      • PYROE MAKE-SPLICED+INTRONIC
      • PYROE MAKE-SPLICED+UNSPLICED
    • QUALIMAP
      • QUALIMAP RNASEQ
      • QUALIMAP RNASEQ
    • QUAST
    • RAGTAG
      • RAGTAG-CORRECTION
      • RAGTAG-MERGE
      • RAGTAG-PATH
      • RAGTAG-SCAFFOLD
    • RASUSA
    • RAZERS3
    • RBT
      • RBT COLLAPSE-READS-TO-FRAGMENTS BAM
      • RBT CSV-REPORT
    • REBALER
    • REFERENCE
      • ENSEMBL-ANNOTATION
      • ENSEMBL-SEQUENCE
      • ENSEMBL-VARIATION
    • REFGENIE
    • RSEM
      • RSEM CALCULATE EXPRESSION
      • RSEM GENERATE DATA MATRIX
      • RSEM PREPARE REFERENCE
    • RSEQC
      • INFER_EXPERIMENT
      • READ_DISTRIBUTION
      • READ_DUPLICATION
      • READ_GC
    • RUBIC
    • SALMON
      • DECOYS
      • SALMON_INDEX
      • SALMON QUANT
    • SALSA2
    • SAMBAMBA
      • SAMBAMBA FLAGSTAT
      • SAMBAMBA INDEX
      • SAMBAMBA MARKDUP
      • SAMBAMBA MERGE
      • SAMBAMBA SLICE
      • SAMBAMBA SORT
      • SAMBAMBA VIEW
    • SAMTOOLS
      • SAMTOOLS CALMD
      • SAMTOOLS DEPTH
      • SAMTOOLS FAIDX
      • SAMTOOLS FASTQ INTERLEAVED
      • SAMTOOLS FASTQ SEPARATE
      • SAMTOOLS FASTX
      • SAMTOOLS FIXMATE
      • SAMTOOLS FLAGSTAT
      • SAMTOOLS IDXSTATS
      • SAMTOOLS INDEX
      • SAMTOOLS MERGE
      • SAMTOOLS MPILEUP
      • SAMTOOLS SORT
      • SAMTOOLS STATS
      • SAMTOOLS VIEW
    • SEQKIT GENERIC WRAPPER
    • SEQTK
    • SHOVILL
    • SICKLE
      • SICKLE PE
      • SICKLE SE
    • SNP-MUTATOR
    • SNPEFF
      • SNPEFF
      • SNPEFF DOWNLOAD
    • SNPSIFT
      • SNPSIFT ANNOTATE
      • SNPSIFT DBNSFP
      • SNPSIFT GENES SETS
      • SNPSIFT GWAS CATALOG
      • SNPSIFT VARTYPE
    • SORTMERNA
    • SOURMASH
      • SOURMASH_COMPUTE
    • SPADES
      • METASPADES
    • SRA-TOOLS
      • SRA-TOOLS FASTERQ-DUMP
    • STAR
      • STAR
      • STAR INDEX
    • STRELKA
      • STRELKA GERMLINE
      • STRELKA
    • STRLING
      • STRLING CALL
      • STRLING EXTRACT
      • STRLING INDEX
      • STRLING MERGE
    • SUBREAD
      • SUBREAD FEATURECOUNTS
    • TABIX
      • TABIX INDEX
      • TABIX QUERY
    • TRANSDECODER
      • TRANSDECODER LONGORFS
      • TRANSDECODER PREDICT
    • TRIM_GALORE
      • TRIM_GALORE-PE
      • TRIM_GALORE-SE
    • TRIMMOMATIC
      • TRIMMOMATIC PE
      • TRIMMOMATIC SE
    • TRINITY
    • TXIMPORT
    • UCSC
      • BEDGRAPHTOBIGWIG
      • FATOTWOBIT
      • GENEPREDTOBED
      • GTFTOGENEPRED
      • TWOBITINFO
      • TWOBITTOFA
    • UMIS
      • UMIS BAMTAG
    • UNICYCLER
    • VARDICT
    • VARSCAN
      • VARSCAN MPILEUP2INDEL
      • VARSCAN MPILEUP2SNP
      • VARSCAN SOMATIC
    • VCFTOOLS
      • VCFTOOLS FILTER
    • VEMBRANE
      • VEMBRANE FILTER
      • VEMBRANE TABLE
    • VEP
      • VEP ANNOTATE
      • VEP DOWNLOAD CACHE
      • VEP DOWNLOAD PLUGINS
    • VERIFYBAMID
      • VERIFYBAMID2
    • VG
      • VG CONSTRUCT
      • VG IDS
      • VG INDEX GCSA
      • VG INDEX XG
      • VG KMERS
      • VG MERGE
      • VG PRUNE
      • VG SIM
    • VSEARCH
    • WGSIM
    • WHATSHAP
      • WHATSHAP HAPLOTAG
    • XSV
  • Meta-Wrappers
    • BOWTIE2 SAMBAMBA
    • BWA_MAPPING
    • CALC_CONSENSUS_READS
    • DADA2-PE
    • DADA2-SE
    • GATK VARIANT CALLING BEST PRACTICE WORKFLOW
    • SALMON TXIMPORT
    • STAR-ARRIBA

Development

  • Contributing
  • Changelog
Snakemake wrappers
/
Wrappers
/
FGBIO

FGBIO

For fgbio, the following wrappers are available:

  • FGBIO ANNOTATEBAMWITHUMIS
  • FGBIO CALLMOLECULARCONSENSUSREADS
  • FGBIO COLLECTDUPLEXSEQMETRICS
  • FGBIO FILTERCONSENSUSREADS
  • FGBIO GROUPREADSBYUMI
  • FGBIO SETMATEINFORMATION

© 2016, The Snakemake team Built with Sphinx 7.2.6