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:map

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

bam:file

BAM/SAM file

*.{bam,sam}

Output

name:type
description
pattern

bam

meta:map

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

*_rmdup.bam:file

Deduplicated BAM file

*_rmdup.bam

json

meta:map

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

*.json:file

JSON file for MultiQC

*.json

hist

meta:map

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

*.hist:file

Histogram data of amount of deduplication

*.hist

log

meta:map

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

*log:file

Dedup log information

*log

versions

versions.yml: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
Github user jfy133
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