Use k-mers to rapidly subtype S. enterica genomes
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}
summary
${prefix}-summary.txt:file
Tab-delimited subtyping summary output
*summary.txt
kmer_results
${prefix}-kmer-results.txt:file
Tab-delimited subtyping kmer matching output
*kmer-results.txt
simple_summary
${prefix}-simple-summary.txt:file
A simple version of summary output
*simple-summary.txt
versions
versions.yml:file
File containing software versions
versions.yml
Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.
