Table I.
Public Tools for In Silico Serotyping Using Whole-Genome Dataa
| Name | Species | Data input | Precision | Website | Refs |
|---|---|---|---|---|---|
| PAst | Pseudomonas aeruginosa | SR or A | Entire locus | github.com/Sandramses/PAst | [102] |
| Kaptive | Klebsiella pneumoniae | A | Entire locus | kaptive.holtlab.net | [4] |
| SerotypeFinder | Escherichia coli | SR or A | wzx/wzy/wzt/wzm | cge.cbs.dtu.dk/services/SerotypeFinder | [103] |
| SRST2 + EcOH | E. coli | SR | wzx/wzy/wzt/wzm | github.com/katholt/srst2 | [104] |
| SeqSero | Salmonella | SR or A | Entire locus | www.denglab.info/SeqSero | [105] |
| SISTR | Salmonella | A | Core genes | lfz.corefacility.ca/sistr-app | [106] |
| PneumoCat | Streptococcus pneumoniae | A | Entire locus | github.com/phe-bioinformatics/PneumoCaT | [107] |
| SeroBA | S. pneumoniae | SR | Entire locus | github.com/sanger-pathogens/seroba | [108] |
a
The list contains publicly available tools for in silico serotyping of WHO priority pathogens listed in Table 1. SR, short-reads; A, assembly.