List of tools

index.md

@@ -5,13 +5,17 @@ title: GAMBIT-suite
 
 # GAMBIT-suite
 
-This repository provides multiple different tools for GAMBIT.
+This organisation provides multiple repositories for tools for [GAMBIT](https://github.com/gambit-suite/gambit) (Genomic Approximation Method for Bacterial Identification and Tracking) which is a tool for rapid taxonomic identification of microbial pathogens.
+
+* [GAMBITtools](https://github.com/gambit-suite/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](https://github.com/gambit-suite/gambitdb): This is a tool to generate a Gambit database. 
+* [GAMBITsizer](https://github.com/gambit-suite/gambitsizer): A tool for estimating the size of an isolate based on the GAMBIT signature.
 
-# GAMBIT databases
 
+# GAMBIT databases
 Details of GAMBIT databases available.
 
-# Bacteria
+## Bacteria
 
 | Release type | Genomes snapshot | Database creation date | Version | Files | Source | Genus | Species | Genomes | More information |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
@@ -20,13 +24,13 @@ Details of GAMBIT databases available.
 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
+## 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
 
 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.