Salmonella In Silico Typing Resource (SISTR) commandline tool database version 1.1.3 used by SISTR release version 1.1.3 and up

Context

Salmonella In Silico Typing Resource (SISTR) commandline tool enables the identification of the Salmonella serovar and cgMLST types of Salmonella from whole genome sequencing (WGS) data tby using a large database (10,000+) of Salmonella genomes and cgMLST profiles based on the 330 alleles. This database is the central part of the SISTR tool and contains both metadata on 2660 serovars and the corresponding antigenic formula, 84463 genomes to serovar mappings, sequences of the O, H1 and H2 antigens, 139729 cgMLST sequences and  38240 profiles with pairwise distances, MASH sketch of the 15465 genomes used for species and serovar identification.

For more information and citation please refer to the following publication and official repository at https://github.com/phac-nml/sistr_cmd/tree/master 

Note: This database was used by SISTR tool up to version 1.1.2 inclusive. From SISTR release 1.1.3 onwards the slightly modified version of this database will be used onwards with changes detailed in https://github.com/phac-nml/sistr_cmd/blob/master/CHANGELOG.md

Citation

The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101

Version changes from v1 to v2

In genomes-to-serovar.txt following serovar changes were made to increase serovar prediction accuracy