https://github.com/jlumpe/gambit
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
https://github.com/jlumpe/gambit
bioinformatics genomics microbiology public-health whole-genome-sequencing
Last synced: about 1 month ago
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A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
- Host: GitHub
- URL: https://github.com/jlumpe/gambit
- Owner: jlumpe
- License: agpl-3.0
- Created: 2021-07-08T23:45:27.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2024-12-02T03:23:33.000Z (6 months ago)
- Last Synced: 2025-03-24T15:47:29.101Z (about 2 months ago)
- Topics: bioinformatics, genomics, microbiology, public-health, whole-genome-sequencing
- Language: Python
- Homepage:
- Size: 6.59 MB
- Stars: 29
- Watchers: 1
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# GAMBIT
[](https://github.com/jlumpe/gambit/actions/workflows/ci.yml)
[](https://gambit-genomics.readthedocs.io/en/latest/?badge=latest)
[](http://bioconda.github.io/recipes/gambit/README.html)
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 © 2016-2024 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 [[email protected]](mailto:[email protected]) 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.