gapit documentation
gapit screens contig files and FASTQ reads for known genes — AMR, virulence, serotype,
plasmid replicons, species targets, or any custom database. It is an agent-first Python
reimplementation of abricate: abricate-compatible
TSV on stdout, plus first-class JSON and Markdown outputs with versioned schemas.
Pages
| Page |
Contents |
| Installation |
PyPI wheel and pixi paths, external binaries, verification, database bootstrap, shell completions |
| Quickstart |
A complete first session on the bundled test fixture, offline |
| Screening contigs |
gapit screen on FASTA/GBK/EMBL inputs: thresholds, filters, formats |
| Screening reads |
FASTQ and assembly FASTA through minimap2: --r1/--r2, presets, breadth-based presence, two-stage survey |
| Summary |
gapit summary: gene presence/absence matrix across report tables |
| Databases |
The database catalog, gapit db fetch/list/install, datadirs, native gapit/v1 format, cluster databases (GBK/GFF, typing.json, kaptive) |
| Custom databases |
gapit db build walkthrough: any FASTA to a screenable database, worked examples |
| Typing schemes |
The two-stage designation pipeline (gapit screen then gapit typing) and gapit.typing/2: rule/scheme primitives, the six-scheme cookbook (Doumith, ShigaTyper, meningotype, VP O/K, cholerae, DEC), allele probe tricks, calibration |
| Outputs |
TSV/JSON/Markdown formats, schemas, error envelopes, exit codes |
| MCP server |
gapit mcp: analysis + database tools for agent runtimes over stdio JSON-RPC |
| Agent guide |
Consuming gapit from autonomous agents: schemas, introspection, errors |
| FAQ |
Common questions, abricate differences, troubleshooting |
Commands
| Command |
What it does |
Docs |
gapit screen |
Screen contig files or FASTQ reads for known genes |
Screening |
gapit typing |
Designate phenotypes from screen result table(s) (typed gene databases) |
Typing schemes |
gapit summary |
Summarize report table(s) into a gene presence/absence matrix |
Summary |
gapit db fetch |
Fetch and build database(s) into the datadir (kaptive cluster dbs download on fetch) |
Databases |
gapit db list |
List known databases (NAME, upstream PROVIDER, install state) |
Databases |
gapit db install |
Install a local file after verifying its SHA256 |
Databases |
gapit db build |
Build a database from a gene FASTA, or from GBK/GFF loci as a cluster database (optionally with a --typing phenotype spec) |
Custom databases |
gapit setupdb |
Build BLAST indices for all databases under the datadir |
here |
gapit schema |
Print the JSON Schema of a gapit output document (report, typing_result, reads, reads2, cluster, summary, error, version, features, typing, floors) |
Outputs |
gapit mcp |
Run the MCP stdio server (also installed as the gapit-mcp console script) |
MCP server |
Project documents
| File |
Contents |
| README |
Project overview, install, quick start, output contract, database table |
| SPEC.md |
The abricate behavior spec; source of truth for parity |
| PLAN.md |
Development roadmap, phase by phase |
| AGENTS.md |
Contributor and agent guide: layout, conventions, verification |
| CHANGELOG.md |
Change history |