FlavoTyper

FlavoTyper is a command-line bioinformatics tool that performs in silico serotyping of Flavobacterium psychrophilum genome assemblies.

About FlavoTyper

Flavobacteriosis is a bacterial disease with significant impact on the global aquaculture industry, particularly affecting salmonids such as rainbow trout and Atlantic salmon. It causes substantial economic losses in fish farms worldwide.

The causative agent is Flavobacterium psychrophilum, a Gram-negative, rod-shaped psychrotrophic bacterium belonging to the family Flavobacteriaceae of the phylum Bacteroidota.

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 is based on previously published data, including the multiplex-PCR serotyping scheme of Rochat et al., 2017 and the functional characterization of the O-polysaccharide-encoding locus by Cisar et al., 2019.

Quickstart

1. Place the genome assembly FASTA file(s) you want to type in one directory.

2. Run FlavoTyper:

   flavotyper type --genomes path/to/genomes/ --outdir results/
   

3. View results — the main output is results/typing_results.tsv.

Where to next

• Installation — Bioconda, PyPI, or from source
• Usage — inputs and the full command reference
• Output files — what each result file contains and how to read it
• How it works — the QC, typing, and locus-analysis modules and the databases
• Results dictionary — full TSV column reference
• Troubleshooting — common errors and questions

Citation

If you use FlavoTyper in a publication or report, please cite the software metadata in CITATION.cff.

License

Apache-2.0. See LICENSE.