Usage

Data input

FlavoTyper accepts genome assemblies for F. psychrophilum in FASTA format (.fa, .fna, .fasta, .fas, optionally gzip-compressed). Both single-genome and multi-genome runs are supported:

# Single genome
flavotyper type --genomes genome.fasta --outdir results/

# Multiple genomes from a directory (all supported extensions are discovered automatically)
flavotyper type --genomes genomes/ --outdir results/ --threads 4

Sample identifiers are derived automatically from input filename stems.

To also generate the locus comparison (alignment, extracted FASTA, and PNG map) for Resolved calls, add --locus-analysis:

flavotyper type --genomes genomes/ --outdir results/ --locus-analysis --threads 4

Command reference

Run flavotyper type --help for the full CLI reference.

Option	Default	Description
--genomes	required	One or more genome FASTA files, or a directory (.fa, .fna, .fasta, .fas, optionally .gz — discovered automatically)
--outdir	required	Output directory
--db	built-in	Path to the serotyping rules YAML
--species-refs	built-in	Reference FASTA for the fastANI species check
--no-species-check	off	Disable F. psychrophilum species validation
--ani-threshold	95.0	Minimum ANI to pass the species gate
--min-identity	97.0	Minimum BLASTN percent identity for marker hits
--min-coverage	94.0	Minimum marker coverage (%) for marker hits
--threads	1	Threads passed to BLASTN and fastANI
--locus-analysis	off	Enable locus comparison and PNG map generation
--locus-db	built-in	Override the built-in reference-locus FASTA
--allow-duplicate-sample-names	off	Allow duplicate IDs from filename stems