Description

Removes alignments to the same position in the genome from the Bismark mapping output.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file containing read alignments

*.{bam}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Deduplicated output BAM file containing read alignments

*.{deduplicated.bam}

report (file)

Bismark deduplication reports

*.{deduplication_report.txt}

versions (file)

File containing software versions

versions.yml
included in
methylseq
maintainer
Github user phue
get in touch
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Tools

bismark
GPL-3.0-or-later

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

github.com/FelixKrueger/Bismark github.com/FelixKrueger/Bismark[...]Docs 10.1093/bioinformatics/btr167