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GAMBIT

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) to identify genome assemblies from across the Bacterial kingdom in seconds.

See below for basic installation and usage instructions, or check out the documentation for more detailed information and a basic tutorial.

About

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. 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 for a reproducible workflow to generate all analyses and figures in the paper.

Contact

Please contact Jared Lumpe at 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:

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.