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.

• Version: 1.1.0
• Added: November, 2025
• Link: https://github.com/jlumpe/gambit

See which versions are available:

$ module avail gambit

Load one version into your environment and run it:

$ module load kleborate/3.2.4
$ gambit

Notes from the sysadmin during installation:

$ cd /var/scratch/aorth/
$ git clone https://github.com/jlumpe/gambit.git -b v1.1.0
$ cd gambit
$ module load python/3.10
$ sudo mkdir -p /export/apps/gambit/1.1.0
$ sudo chown aorth:aorth /export/apps/gambit/1.1.0
$ python -m venv /export/apps/gambit/1.1.0/venv
$ source /export/apps/gambit/1.1.0/venv/bin/activate
$ pip install -U pip wheel setuptools
$ pip install .
$ mkdir /export/apps/gambit/1.1.0/db
$ wget https://storage.googleapis.com/jlumpe-gambit/public/databases/refseq-curated/1.0/gambit-refseq-curated-1.0.gdb -O /export/apps/gambit/1.1.0/db/gambit-refseq-curated-1.0.gdb
$ wget https://storage.googleapis.com/jlumpe-gambit/public/databases/refseq-curated/1.0/gambit-refseq-curated-1.0.gs -O /export/apps/gambit/1.1.0/db/gambit-refseq-curated-1.0.gs
$ sudo chown -R root:root /export/apps/gambit/1.1.0