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Snakemake wrappers

Wrappers and Meta-Wrappers

Wrappers
- ADAPTERREMOVAL
- ARRIBA
- ART
- ASSEMBLY-STATS
- BAMTOOLS
- BARRNAP
- BAZAM
- GENERIC
- BCFTOOLS
- BEDTOOLS
- BELLEROPHON
- BENCHMARK
- BGZIP
- BIOBAMBAM2
- 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
  - 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
- SORTMERNA
- 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

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Wrappers
EPIC

EPIC#

For epic, the following wrappers are available:

EPIC

Snakemake homepage Snakemake documentation

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