Output files¶

All output files are written to the directory specified with --outdir.

Tabular format (TSV)¶

typing_results.tsv — the main output table, one row per sample.

Key columns include the assigned serotype, call state (Resolved / Partial / Ambiguous / NotTyped), detected markers, QC metrics, typing warnings, and a reference sentence for known serotypes. For the full column reference, see the Results dictionary.

JSON format¶

typing_results.jsonl — one complete JSON record per sample (same data as the TSV, machine-readable).
run_metadata.json — run-level provenance: tool version, database name and checksums, parameters, run ID, and timestamp.
input_manifest.json — per-input manifest: source path, file size, and SHA-256 checksum.

Locus-analysis outputs (optional)¶

When a call is Resolved and locus analysis is enabled (--locus-analysis), the tool also produces, per sample:

<sample>_locus_sequence.fasta — the O-antigen biosynthesis locus extracted from the input genome.
<sample>_locus_map.png — a two-track locus map showing the reference locus alongside the aligned sample region, with annotated marker positions.
<sample>_locus_alignment.txt — pairwise BLASTN alignment of the sample genome against the reference locus.

These are written to a per-sample subdirectory, <outdir>/<sample>_locus_analysis/.

Directory layout¶

results/
├── typing_results.tsv
├── typing_results.jsonl
├── run_metadata.json
├── input_manifest.json
├── sample1_locus_analysis/          # only when --locus-analysis is enabled
│   ├── sample1_locus_map.png
│   ├── sample1_locus_alignment.txt
│   └── sample1_locus_sequence.fasta
└── sample2_locus_analysis/
    ├── sample2_locus_map.png
    ├── sample2_locus_alignment.txt
    └── sample2_locus_sequence.fasta

Interpreting the call state¶

`Call_state`	Meaning
`Resolved`	O-type and R-type were both uniquely assigned
`Partial`	One of O or R is `Undefined` — check `Typing_warnings` and assembly quality
`Ambiguous`	One of O or R matched multiple valid interpretations — check `Alternative_serotypes`
`NotTyped`	QC blocked typing — check `QC_warnings` and the species fields

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