Description

Merging overlapping paired reads into a single read.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

reads:file

List of input paired end fastq files

*.{fastq,fq}.gz

interleave:boolean

Indicates whether the input paired reads are interleaved or not

Output

name:type
description
pattern

merged

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_merged.fastq.gz:file

merged reads

*_merged.fastq

unmerged

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_unmerged.fastq.gz:file

unmerged reads

*_unmerged.fastq

ihist

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_ihist.txt:file

insert size histogram

*_ihist.txt

versions

versions.yml:file

File containing software versions

versions.yml

log

*.log:file

log file containing stdout and stderr from bbmerge.sh

*.log

Tools

bbmap
UC-LBL license (see package)

BBMap is a short read aligner, as well as various other bioinformatic tools.