Description

Adapter and quality trimming of 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 1 and 2 for single-end and paired-end data,
respectively.

contaminants (file)

Reference files containing adapter and/or contaminant sequences for sequence kmer matching

Output

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

The trimmed/modified fastq reads

*fastq.gz

versions (file)

File containing software versions

versions.yml

log (file)

Bbduk log file

*bbduk.log
included in
metatdenovo taxprofiler
author
Github user MGordon09
get in touch
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Tools

bbmap
UC-LBL license (see package)

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

jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide