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How it works

FlavoTyper runs each sample through up to three modules: a QC gate, the typing engine, and (optionally) locus analysis.

QC module

This first module ensures that:

  1. the input genome corresponds to the species Flavobacterium psychrophilum, and
  2. the genome assembly quality allows a reliable serotype assignment.

Samples that fail QC are recorded as NotTyped in the output and skip the typing step.

Species check (enabled by default)

An ANI-based species validation step using fastANI is run before typing. The input genome is compared against the F. psychrophilum type-strain reference genome (NCIMB 1947T). Genomes below the ANI threshold (default: 95 %) are blocked from further typing.

This step can be disabled with --no-species-check when species identity has been confirmed independently.

Assembly quality check

Before typing, FlavoTyper evaluates assembly quality:

  • Genome size — flagged if outside the expected interval [2,619,202 – 3,122,663 bp], derived from a curated reference set.
  • Contig count — advisory warning above 300 contigs; high-severity warning above 500 contigs.
  • GC percent — reported for the provided genome(s).

The assembly quality check is advisory only; it provides informative warnings about metrics that might affect the reliability of serotype assignment.

Typing module

The core module detects serotype-associated marker genes with BLASTN against the built-in marker database, then applies a declarative rule engine to assign serotype components independently:

  • O-type — assigned from the exclusive detection of one O-antigen marker (a wzy gene).
  • R-type — assigned from base-group marker presence (R1, R2, R3, R4) and optional inter-marker distance rules for variant confirmation (R1V1, R1V2, R1V3).
  • S-type — assigned independently from the S1 marker: S0 when absent, S1 when present.

The combined serotype is reported as O:X-Sy-Rz (e.g. O:1-S0-R1V1).

Locus analysis module (optional, --locus-analysis)

When a call is Resolved and this module is enabled, a second BLASTN aligns the genome against a full O-antigen biosynthesis locus from a reference strain. This produces a pairwise alignment text file, the extracted locus FASTA, and a two-track PNG locus map.

Novel serotypes (not yet in the reference-locus database) are flagged with a warning in Typing_warnings but are not blocked from receiving a type call.

Databases

All reference data is bundled with the FlavoTyper package. The built-in data directory can be retrieved with:

flavotyper data-dir

Flavotyper_markers.fasta

Nucleotide sequences for all marker genes used by the typing module; the BLAST database is built from this file at runtime.

A marker is considered present when a BLASTN hit meets both thresholds: percent identity ≥ 97 % and marker coverage ≥ 94 % (adjustable via --min-identity and --min-coverage).

Markers currently covered:

  • O-type — each type (O:0–O:7) is detected by a unique wzy gene (wzy0–wzy7).
  • R-type — R0 is the default when no R markers are detected (only observed in O:0). R1 variants share a common r1_core marker and are further distinguished by wfpF (R1V1); Rieske + wfpF_p within −6 to +6 bp of each other (R1V2); wfpF_pp (R1V3). R2, R3, and R4 are each assigned from a single marker: wfpH, wfpI, and r4_core respectively.
  • S-type — S1 is assigned when s1_core is detected; S0 when absent.

Flavotyper_reference_loci.fasta

Full nucleotide sequences of reference O-antigen biosynthesis loci for each known serotype, with embedded metadata (reference strain, genome coordinates, GenBank accession, PMID, and per-marker positions). Used by the locus analysis module.