Description

Generate k-mers (sketches) from FASTA/Q sequences

Input

Name (Type)
Description
Pattern

meta (map)

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

]

sequences (file)

fasta file, or a directory containing FASTA files

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

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

outdir (directory)

Output directory containing all .unik files and a summary file in .txt format. Every .unik file contains the sequence/reference ID,chunk index, number of chunks, and genome size of reference.

*/

info (file)

Summary file that is generated for later use

*_info.txt
author
Github user sofstam
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Tools

kmcp
MIT

Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

github.com/shenwei356/kmcp github.com/shenwei356/kmcp#documents https://github.com/shenwei356/kmcp 10.1093/bioinformatics/btac845