FlavoTyper

FlavoTyper is a bioinformatics tool that performs in silico serotyping of Flavobacterium psychrophilum genome assemblies. Phenotypic characterization of this pathogen (including serotyping based on the structural variations in the O-polysaccharide moiety of cell surface lipopolysaccharide) provides critical information for epidemiological surveillance, outbreak investigation, and the design of effective vaccines. FlavoTyper enables this characterization directly from genome assemblies, making serotyping scalable, reproducible, and independent of wet-lab assays.

FlavoTyper was developed by Salma Mbarki in the Laboratory of Eric Duchaud, Unité Virologie et Immunologie Moléculaires (INRAE), France. The code can be found at https://pypi.org/project/flavotyper/.

The tool will only be enabled on the database for Flavobacterium psychrophilum.

The function can be accessed by expanding the ‘Analysis’ section on the main contents page.

Alternatively, it can be accessed following a query by clicking the ‘Gene Presence’ button at the bottom of the results table. Isolates returned from the query will be automatically selected within the plugin interface.

Finally, the analysis is also possible directly from an isolate record, if the isolate has a genome assembly associated with it.

The tool interface consists of a list of isolate ids to check. This will be pre-populated if accessed following a query or directly from an isolate record.

Click ‘submit’.

The output will be an HTML table (if fewer than 100 records are selected), a tab-delimited text file and an Excel file generated from this.

If a single record is chosen, the output may also include a .png file of a two- track locus map.

The results from running FlavoTyper will be stored in the database and once run are available for display within an isolate record.