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
gzipped fasta file. If files are NOT in
MiSeq format sample_S1_L001_R1_001.fastq.gz uses —forward and —reverse parameters; otherwise
default is _1, i.e. expect forward reads as sample_1.fastq.gz).
*.fastq.gz maintainer
