Description

Perform merging of mate paired-end sequencing reads

Input

name:type
description
pattern

meta:map

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

]

reads:file

List of input FastQ files of size 2; i.e., paired-end data.

*fastq.gz

Output

name:type
description
pattern

merged

meta:map

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

]

${prefix}.extendedFrags.fastq.gz:file

The merged fastq reads

.extendedFrags.fastq.gz

notcombined

meta:map

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

]

${prefix}.notCombined_*.fastq.gz:file

Not combined reads from flash

.notCombined_*.fastq.gz

histogram

meta:map

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

]

${prefix}.hist:file

HistogramNumeric histogram of merged read lengths.

.hist

versions

versions.yml:file

File containing software versions

versions.yml

Tools

flash
GPL v3+

Merge mates from fragments that are shorter than twice the read length