modules/srst2_srst2
Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
Description
Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
Input
Groovy Map containing sample information id: should be the identification number or sample name single_end: should be true for single end data and false for paired in data db: should be either ‘gene’ to use the —gene_db option or “mlst” to use the —mlst_db option e.g. [ id:‘sample’, single_end
, db:‘gene’]