gapit
Mass screening of contigs and reads for known genes — AMR, virulence, serotype, plasmid replicons, species markers, or any custom database. Contig screening emits abricate-compatible TSV; JSON and Markdown are first-class outputs. Python 3.12.
Install
pip install gapit
BLAST+ (blastn, blastx, makeblastdb, blastdbcmd) and minimap2 must be on
PATH. The pixi/conda paths install them for you; see
installation for those, Docker, and pinned setups.
# from a clone, with the external binaries managed for you
git clone https://github.com/indexofire/gapit.git
cd gapit
pixi install
pixi run gapit --version
Quick start
Bundled databases work offline on first use; every other database is fetched with
gapit db fetch.
# contigs -> abricate-compatible TSV on stdout
gapit screen contigs.fa --db eco_dec
# JSON / Markdown for agents and humans
gapit screen contigs.fa --db eco_dec --format json
gapit screen contigs.fa --db eco_dec --format md
# FASTQ reads through minimap2
gapit screen --r1 R1.fastq.gz --r2 R2.fastq.gz --read-type sr --db eco_dec
# two-stage gene typing: screen writes the table, typing designates from it
gapit screen isolate.fa --db eco_dec --output result.tsv
gapit typing result.tsv
# summarize many reports into a gene matrix
gapit summary *.tsv
# databases
gapit db fetch -d ncbi
gapit db list
# introspect the output contract
gapit schema report
Contig defaults are --minid 80 --mincov 80; reads presence defaults to 90% alignment
breadth. Full flags and examples: contigs, reads,
typing, summary.
Documentation
| Topic | Page |
|---|---|
| Install, quickstart | installation, quickstart |
| Contig screening, cluster databases | screen |
| Reads and assembly surveys | reads |
| Gene matrices | summary |
| Typing schemes and phenotypes | typing |
| JSON/Markdown contracts, error envelope | outputs, gapit schema |
| Database catalog, providers, bundles | databases |
| Datadir, sharing, Docker | datadir |
| Custom databases | custom-db |
| Agents and MCP server | agents, mcp |
| Optional gseek engine | gseek |
Full manual: https://indexofire.github.io/gapit/.
Development and license
Contributor workflow and gates: CONTRIBUTING.md; internal rules: AGENTS.md; trust boundaries: SECURITY.md; changes: CHANGELOG.md.
gapit is MIT-licensed. It is a behavioral reimplementation of abricate (GPL-2.0) and copies no Perl code. The seven gapit-curated bundled databases are permissively licensed; every other provider downloads from upstream at fetch time under its own license. If you use gapit, cite CITATION.cff.
1 maintainer
Metadata
1 maintainer
Release files for gapit 0.6.8
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| gapit-0.6.8.tar.gz | 3.2 MB | With provenance | Details for gapit-0.6.8.tar.gz |
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| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| gapit-0.6.8-py3-none-any.whl | Python 3 | none | any | Details for gapit-0.6.8-py3-none-any.whl |
Total release size: 6.0 MB
Release files / gapit-0.6.8.tar.gz
| Download URL | gapit-0.6.8.tar.gz |
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| Size | 3.2 MB |
| Tags | Source |
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| Tags | Python 3 |
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