Table 3 List of different tools for in silico serovar prediction
Tool (Reference) | Species | Method | Source |
|---|---|---|---|
SeqSero [137] | Salmonella spp. | mapping of raw reads to database of O and H antigen alleles | command line: https://github.com/denglab/SeqSero |
Web tool: http://denglab.info/SeqSero | |||
SeqSero2 [138] | Salmonella spp. | similar SeqSero, additional performs rapid serotype prediction based on unique k-mers of serotype determinants | command line: https://github.com/denglab/SeqSero2 |
Salmonella TypeFinder | Salmonella spp. | in addition to running SeqSero, determines 7 gene MLST and infers serovar from sequence type according to Enterobase database | Web tool: https://cge.cbs.dtu.dk/services/SalmonellaTypeFinder/ |
SISTR [139] | Salmonella spp. | mapping of database of O and H antigen alleles against genome assembly, additionally, determines cgMLST and infers serovar from cgMLST clustering result | command line: https://github.com/phac-nml/SISTR_cmd |
Web tool: https://lfz.corefacility.ca/sistr-app/ | |||
MOST [140] | Salmonella spp. | determines 7-gene MLST and reports number of respective serovar – ST matches from the PHE/Achtmann database | command line: https://github.com/phe-bioinformatics/MOST |
Serotype Finder [141] | E. coli | mapping of raw reads to database of O and H antigen alleles, or mapping of antigen alleles against genome assembly | command line: https://github.com/Papos92/ecoli_serotyper |
Web tool: https://cge.cbs.dtu.dk/services/SerotypeFinder/ | |||
ECTyper | E. coli | Information not available | command line: https://github.com/phac-nml/ecoli_serotyping |
EBEis from the Enterobase Tool Kit | E. coli Shigella spp. | mapping of database of O and H antigen alleles against genome assembly | command line: https://github.com/zheminzhou/EToKi#ebeis%2D%2D-in-silico-serotype-prediction-for-escherichia-coli%2D%2Dshigella-spp |
Seq_typing | E. coli | mapping of raw reads to database of O and H antigen alleles, or mapping of antigen alleles against genome assembly | command line: https://github.com/B-UMMI/seq_typing |
LisSero [134] | Listeria monocytogenes | mapping of database of 5 DNA regions (lmo1118, lmo0737, ORF2110, ORF2819, prs) against genome assembly | command line: https://github.com/MDU-PHL/LisSero |