Snakemake Wrappers
v2.12.0

Wrappers and Meta-Wrappers

  • Wrappers
    • ADAPTERREMOVAL
    • ARRIBA
    • ART
    • ASSEMBLY-STATS
    • BAMTOOLS
    • BARRNAP
    • BAZAM
    • BBTOOLS
    • BCFTOOLS
    • BEDTOOLS
    • BELLEROPHON
    • BENCHMARK
    • BGZIP
    • BIOBAMBAM2
    • BISMARK
      • BAM2NUC
      • BISMARK
      • BISMARK2BEDGRAPH
      • BISMARK2REPORT
      • BISMARK2SUMMARY
      • BISMARK_GENOME_PREPARATION
      • BISMARK_METHYLATION_EXTRACTOR
      • DEDUPLICATE_BISMARK
    • BLAST
    • BOWTIE2
    • BUSCO
    • BUSTOOLS
    • BWA
    • BWA-MEM2
    • BWA-MEME
    • BWA-MEMX
    • CAIROSVG
    • CLUSTALO
    • CNV_FACETS
    • CNVKIT
    • COOLPUP.PY
    • COOLTOOLS
    • CUTADAPT
    • DADA2
    • DATAVZRD
    • DEEPTOOLS
    • DEEPVARIANT
    • DELLY
    • DESEQ2
    • DIAMOND
    • DRAGMAP
    • ENCODE_FASTQ_DOWNLOADER
    • ENHANCED VOLCANO
    • EPIC
    • FASTP
    • FASTQ_SCREEN
    • FASTQC
    • FASTTREE
    • FGBIO
    • FILTLONG
    • FREEBAYES
    • GALAH
    • GATK
    • GATK3
    • GDC-API
    • GDC-CLIENT
    • GENEFUSE
    • GENOMEPY
    • GENOMESCOPE
    • GFATOOLS
    • GFFREAD
    • GRIDSS
    • GSEAPY
    • HAP.PY
    • HIFIASM
    • HISAT2
    • HMMER
    • HOMER
    • IGV-REPORTS
    • IMMUNEDECONV
    • INFERNAL
    • JANNOVAR
    • JELLYFISH
    • KALLISTO
    • LAST
    • LIFTOFF
    • LOFREQ
    • MACS2
    • MANTA
    • MAPDAMAGE2
    • MASHMAP
    • MERQURY
    • MERYL
    • METHYLDACKEL
    • MICROPHASER
    • MINIMAP2
    • MLST
    • MOSDEPTH
    • MSISENSOR
    • MULTIQC
    • MUSCLE
    • NANOSIM-H
    • NEXTFLOW
    • NGS-DISAMBIGUATE
    • NONPAREIL
    • OPEN-CRAVAT
    • OPTITYPE
    • PALADIN
    • PANDORA
    • PBMM2
    • PEAR
    • PICARD
    • PINDEL
    • PLASS
    • PRESEQ
    • PRETEXT
    • PRIMERCLIP
    • PROSOLO
    • PTRIMMER
    • PURGE_DUPS
    • PYFASTAQ
    • PYROE
    • QUALIMAP
    • QUAST
    • RAGTAG
    • RASUSA
    • RAZERS3
    • RBT
    • REBALER
    • REFERENCE
    • REFGENIE
    • RSEM
    • RUBIC
    • SALMON
    • SALSA2
    • SAMBAMBA
    • SAMTOOLS
    • SEQKIT GENERIC WRAPPER
    • SEQTK
    • SHOVILL
    • SICKLE
    • SNP-MUTATOR
    • SNPEFF
    • SNPSIFT
    • SOURMASH
    • SPADES
    • SRA-TOOLS
    • STAR
    • STRELKA
    • STRLING
    • SUBREAD
    • TABIX
    • TRANSDECODER
    • TRIM_GALORE
    • TRIMMOMATIC
    • TRINITY
    • TXIMPORT
    • UCSC
    • UMIS
    • UNICYCLER
    • VARDICT
    • VARSCAN
    • VCFTOOLS
    • VEMBRANE
    • VEP
    • VERIFYBAMID
    • VG
    • VSEARCH
    • WGSIM
    • WHATSHAP
    • XSV
  • Meta-Wrappers

Development

  • Contributing
Snakemake Wrappers
  • Wrappers
  • BISMARK
  • Edit on GitHub

BISMARK

For bismark, the following wrappers are available:

  • BAM2NUC
  • BISMARK
  • BISMARK2BEDGRAPH
  • BISMARK2REPORT
  • BISMARK2SUMMARY
  • BISMARK_GENOME_PREPARATION
  • BISMARK_METHYLATION_EXTRACTOR
  • DEDUPLICATE_BISMARK
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