Description

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

Input bam file

*.bam

bai{:bash}

:file

BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input.

*.{bai}

mode{:bash}

:string

Selects the mode of Umicollapse - either fastq or bam need to be provided.

{fastq,bam}

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

BAM file with deduplicated UMIs.

*.{bam}

fastq{:bash}

meta{:bash}

:map

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

*dedup*fastq.gz{:bash}

:file

FASTQ file with deduplicated UMIs.

*dedup*fastq.gz

log{:bash}

meta{:bash}

:map

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

*_UMICollapse.log{:bash}

:file

A log file with the deduplication statistics.

*_{UMICollapse.log}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

umicollapse
MIT

UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs).

github.com/Daniel-Liu-c0deb0t/UMICollapse https://github.com/siddharthab/UMICollapse 10.7717/peerj.8275
included in
lncpiperiboseqrnaseqsmrnaseq
maintainers
Github user CharlotteAnne
Github user chris-cheshire
Github user apeltzer
Github user siddharthab
Github user MatthiasZepper
get in touch
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