Description

Align short or PacBio reads to a reference genome using BBMap

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fastq (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

ref (file)

Either “ref” a directory containing an index, the name of another directory
with a “ref” subdirectory containing an index or the name of a fasta formatted
nucleotide file containg the reference to map to.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

BAM file

*.{bam}
included in
metatdenovo
author
Github user erikrikarddaniel
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