gambit-suite.github.io

GAMBIT-suite

This organisation provides multiple repositories for tools for GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) which is a tool for rapid taxonomic identification of microbial pathogens.

• GAMBITtools: This repository contains a collection of tools for working with GAMBIT. The tools are written in Python and are designed to be used in conjunction with GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) which is a tool for rapid taxonomic identification of microbial pathogens.
• GambitDB: This is a tool to generate a Gambit database.
• GAMBITsizer: A tool for estimating the size of an isolate based on the GAMBIT signature.

GAMBIT databases

Details of GAMBIT databases available.

Bacteria

Release type	Genomes snapshot	Database creation date	Version	Files	Source	Genus	Species	Genomes	More information
Depreciated	2016	2022-10-08	1.0	https://storage.googleapis.com/jlumpe-gambit/public/databases/refseq-curated/1.0/gambit-refseq-curated-1.0.gs https://storage.googleapis.com/jlumpe-gambit/public/databases/refseq-curated/1.0/gambit-refseq-curated-1.0.gdb	NCBI	452	1415	43195	https://doi.org/10.1371/journal.pone.0277575
Latest	2023-04-17	????	1.1.0	gs://theiagen-public-files/terra/gambit_files/1.1.0/gambit-signatures-1.1-230417.gs
gs://theiagen-public-files/terra/gambit_files/1.1.0/gambit-metadata-1.1-230417.gdb	NCBI	454	1530	47063	https://www.notion.so/GAMBIT-RefSeq-Curated-Database-v1-1-0-b5af62c6bcb544b48501752f2e741b21?pvs=21
Testing	GTDB r214, NCBI xxxx		1.2.2		NCBI/GTDB	1651	5429	65425	Novel species added from GTDB to expand species coverage.

Fungal

Date	Version	Files	Source	Genus	Species	Genomes	More information
2022-11-30	0.2	https://storage.cloud.google.com/theiagen-public-files-rp/terra/theiaeuk-files/gambit/221130-theiagen-fungal-v0.2.h5https://storage.cloud.google.com/theiagen-public-files-rp/terra/theiaeuk-files/gambit/221130-theiagen-fungal-v0.2.db	NCBI	138	245	5359	https://doi.org/10.3389/fpubh.2023.1198213paper

Archaea

Archaea are poorly represented in the public archives and the databases here should be used with caution. For the most part only 1 genome is available per species/genus and the genus/species only have candidate names. As the genomes are mostly derived from uncultured samples quality criteria had to be eased.

Genomes snapshot date	Version	Files	Source	Genus	Species	Genomes
2023-10-10	1.0.0	https://storage.cloud.google.com/ajp_gambit_db/archaea/gambit-archaea-signatures-1.0.0-20231009.gs https://storage.cloud.google.com/ajp_gambit_db/archaea/gambit-archaea-metadata-1.0.0-20231009.gdb	GTDB - 214.1	361	750	2679