Description

Performs fastq alignment to a fasta reference using NextGenMap

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, if meta.single_end is true, and 2
if meta.single_end is false.

fasta (file)

Genomic reference fasta file

*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information. First item of tuple with
bam, below.
e.g. [ id:‘test’, single_end

]

bam (file)

Output BAM file containing read alignments. Second item of tuple with
meta, above

*.{bam}

versions (file)

File containing software versions

versions.yml
author
Github user cmatkhan
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Tools

bwa
MIT

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime

github.com/Cibiv/NextGenMap github.com/Cibiv/NextGenMap/wiki 10.1093/bioinformatics/btt468