Fig. 1
From: Determining Streptococcus suis serotype from short-read whole-genome sequencing data
Schematic of the S. suis serotyping pipeline. The pipeline takes in S. suis WGS reads in fastq format and first confirms that the isolate belongs to the species S. suis by aligning reads to the gene recN using SRST2 software. Once species has been confirmed, SRST2 is invoked in three parallel instances to identify serotype, MLST information, and virulence gene content using provided databases. The serotyping component cannot differentiate between serotype 1 and serotype 14, or between serotype 2 and serotype 1/2 without additional comparison of the sequences of the cps2K gene (see results). Final serotype determination results are then combined with MLST and virulence results to provide the user a single output file