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

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. 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

Conda

Install from Bioconda:

conda install -c conda-forge -c bioconda gambit

Pixi

Install the gambit command globally using Pixi:

pixi global install -c conda-forge -c bioconda gambit

To add GAMBIT to an existing Pixi workspace instead, use pixi add gambit (after ensuring the conda-forge and bioconda channels are added to the workspace).

Pip

pip install gambit

Pre-built wheels are only provided for Linux (x86_64) and CPython 3.12-3.14. On other platforms pip will attempt to build from the source distribution (see next section).

From source

git clone https://github.com/jlumpe/gambit.git
cd gambit
pip install .  # or "pip install -e ." for an editable install

Requires a C compiler with OpenMP support. Not supported on macOS (Apple clang lacks -fopenmp) or Windows. macOS users should install using Conda or Pixi instead, and Windows users should use WSL.

Database files

GAMBIT requires a reference database for taxonomic identification. Download the database files and place them in a directory of your choice:

• gambit-refseq-curated-1.0.gdb
• 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.