Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

reads (file)

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

index (directory)

Biscuit genome index directory (generated with 'biscuit index')

BiscuitIndex

Output

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

Output BAM file containing read alignments

*.{bam}

bai (file)

Output BAM index

*.{bai}

versions (file)

File containing software versions

versions.yml
author
Github user njspix
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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/samblaster10.1093/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/samtools10.1093/bioinformatics/btp352