Description

A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

reads{:bash}

:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta{:bash}

:file

Input genome fasta file

meta3{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

index{:bash}

:directory

Directory containing biscuit genome index

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.bam{:bash}

:file

Output BAM file containing read alignments

*.{bam}

bai{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.bai{:bash}

:file

Output BAM index

*.{bai}

versions_biscuit{:bash}

${task.process}{:bash}

:string

The name of the process

biscuit{:bash}

:string

The name of the tool

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'{:bash}

:eval

The expression to obtain the version of the tool

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version |& sed '1!d; s/^.*samtools //'{:bash}

:eval

The expression to obtain the version of the tool

versions_samblaster{:bash}

${task.process}{:bash}

:string

The name of the process

samblaster{:bash}

:string

The name of the tool

samblaster --version |& sed 's/^.*samblaster: Version //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

biscuit{:bash}

:string

The name of the tool

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version |& sed '1!d; s/^.*samtools //'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

samblaster{:bash}

:string

The name of the tool

samblaster --version |& sed 's/^.*samblaster: Version //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

biscuit
MIT

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/biscuitblaster https://github.com/huishenlab/biscuit

samblaster
MIT

samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. By default, samblaster reads SAM input from stdin and writes SAM to stdout.

github.com/GregoryFaust/samblaster 10.1093/bioinformatics/btu314

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352
maintainers
Github user njspix
Github user sateeshperi
get in touch
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