Short Read Sequence Typing for Bacterial Pathogens
This program is designed to take Illumina sequence data, a MLST (Multi Locus Sequence Types) database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs (Serotypes) and/or reference genes
Read more about the tool: https://holtlab.net/2014/12/27/behind-the-paper-srst2-for-short-read-sequence-typing-of-bacterial-pathogens/
Learn more about all inputs and their formates: https://github.com/katholt/srst2#input-read-formats-and-options
Learn more about all outputs: https://github.com/katholt/srst2#output-files