Description

Use k-mers to rapidly subtype S. enterica genomes

Input

name:type
description
pattern

meta:map

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

]

seqs:file

FASTA or FASTQ

*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}

scheme_metadata:file

Scheme subtype metadata table

*.{tab,tsv,txt}

Output

name:type
description
pattern

summary

meta:map

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

]

${prefix}-summary.txt:file

Tab-delimited subtyping summary output

*summary.txt

kmer_results

meta:map

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

]

${prefix}-kmer-results.txt:file

Tab-delimited subtyping kmer matching output

*kmer-results.txt

simple_summary

meta:map

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

]

${prefix}-simple-summary.txt:file

A simple version of summary output

*simple-summary.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

biohansel
Apache-2.0 license

Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.