Use k-mers to rapidly subtype S. enterica genomes
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
seqs
FASTA or FASTQ
*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}
scheme_metadata
Scheme subtype metadata table
*.{tab,tsv,txt}
versions
File containing software versions
versions.yml
summary
Tab-delimited subtyping summary output
*summary.txt
kmer_results
Tab-delimited subtyping kmer matching output
*kmer-results.txt
simple_summary
A simple version of summary output
*simple-summary.txt
Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.
