Metadata-Version: 2.4
Name: gambit
Version: 1.2.0
Summary: Genomic Approximation Method for Bacterial Identification and Tracking
Author-email: Jared Lumpe <jared@jaredlumpe.com>
License-Expression: AGPL-3.0-or-later
Project-URL: Homepage, http://github.com/jlumpe/gambit
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.19
Requires-Dist: sqlalchemy>=1.4
Requires-Dist: biopython~=1.79
Requires-Dist: attrs>=23.1
Requires-Dist: cattrs>=23.2
Requires-Dist: click>=8.0
Requires-Dist: h5py~=3.1
Requires-Dist: scipy~=1.7
Requires-Dist: typing-extensions>=4.1
Dynamic: license-file

# GAMBIT

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GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens.
It uses an efficient genomic distance metric along with a curated database of approximately 50,000 reference genomes (derived from NCBI
[RefSeq](https://www.ncbi.nlm.nih.gov/refseq/)) to identify genome assemblies from across the Bacterial kingdom in seconds.

See below for basic installation and usage instructions, or check out the
[documentation](https://gambit-genomics.readthedocs.io/en/latest) for more detailed information and
a basic tutorial.


## About

Copyright © 2016-2026 Jared Lumpe

GAMBIT has been a personal project of mine for many years. Although there have been numerous
contributors to the publication, it is not a product of any lab or institution.

GAMBIT is provided as free software under the terms of the [AGPLv3 license](LICENSE).
It is not covered by any type of software patent.


### Publication

Lumpe J, Gumbleton L, Gorzalski A, Libuit K, Varghese V, et al. (2023) GAMBIT (Genomic Approximation
Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome
sequencing of bacterial isolates for clinical identification. PLOS ONE 18(2): e0277575.
https://doi.org/10.1371/journal.pone.0277575

See [jlumpe/gambit-publication](https://github.com/jlumpe/gambit-publication) for a reproducible
workflow to generate all analyses and figures in the paper.


### Contact

Please contact Jared Lumpe at [jared@jaredlumpe.com](mailto:jared@jaredlumpe.com) with any questions or feedback.


## Installation

Install the Python library from Bioconda:

```
conda install -c bioconda gambit
```

Then download the reference database files and place them in a directory of your choice:

* [gambit-refseq-curated-1.0.gdb](https://storage.googleapis.com/jlumpe-gambit/public/databases/refseq-curated/1.0/gambit-refseq-curated-1.0.gdb)
* [gambit-refseq-curated-1.0.gs](https://storage.googleapis.com/jlumpe-gambit/public/databases/refseq-curated/1.0/gambit-refseq-curated-1.0.gs)


## Basic usage

    gambit [-d /path/to/database/] query [-o results.csv] genome1.fasta genome2.fasta ...

Positional arguments are one or more FASTA files containing query genome assemblies. You must
provide the path to the directory containing the database files using either the `-d` option
(*before* the `query` subcommand) or by setting the `GAMBIT_DB_PATH` environment variable.

See the documentation for additional details on the command line interface and description of the output.
