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