Description

DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/SAM file

*.{bam,sam}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*_rmdup.bam{:bash}

:file

Deduplicated BAM file

*_rmdup.bam

json{:bash}

meta{:bash}

:map

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

*.json{:bash}

:file

JSON file for MultiQC

*.json

hist{:bash}

meta{:bash}

:map

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

*.hist{:bash}

:file

Histogram data of amount of deduplication

*.hist

log{:bash}

meta{:bash}

:map

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

*log{:bash}

:file

Dedup log information

*log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

dedup
GPL v3

DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).

github.com/apeltzer/DeDup dedup.readthedocs.io/en/latest https://github.com/apeltzer/DeDup 10.1186/s13059-016-0918-z
maintainer
Github user jfy133
get in touch
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