xgt

Efficient querying and parsing of the GTDB database

🗺️ Overview

xgt is a Rust tool that enables efficient querying and parsing of the GTDB database. xgt consists of a collection of commands mirroring the GTDB API and providing additional parsing capability.

📋 Features

search subcommand

It offers both exact and partial matches, along with additional parsing capabilities. Additionally, it supports searching the GTDB using multiple names listed in a plain text file.

genome subcommand

It can be used to retrieve information about a genome. The --metadata option provides concise genome metadata such as accession and surveillance data, while --history retrieves the genome taxon history in the GTDB. The default option fetches nucleotide, gene, and taxonomy metadata of the genome.

taxon subcommand

This tool fetches information about a specific taxon. Users can search for the direct descendants of a taxon and retrieve taxon genomes in the GTDB using partial or exact matches.

Certificate verification

xgt through ureq performs peer SSL certificate verification by default. To tell xgt to not verify the peer, use the -k/--insecure option. Currently (as of Apr 28, 2024), you should add this option to your command to get the desired result as GTDB API's server has a certificate issue.

🔧 Installing

From source

git clone https://github.com/Ebedthan/xgt.git
cd xgt

# If default rust install directory is ~/.cargo
cargo install --path . --root ~/.cargo
xgt -h

Using binaries

Please find the binaries for the latest release using the release page or using the direct link below:

• Apple Silicon macOS with its checksum
• Intel macOS with its checksum
• x64 Windows with its checksum
• x64 Linux with its checksum

💡 Example

# Search subcommand: search GTDB
## Search all Escherichia (genus) genomes
xgt search -kw g__Escherichia

## Search all genomes with genus name containing Escherichia
xgt search -k -o output.csv g__Escherichia

## Search from a list
xgt search -k -f list.txt

# Genome subcommand: information about a genome
## Get GTDB genome information
xgt genome -k GCA_001512625.1

## Get taxon history on GTDB
xgt genome -k --history GCA_001512625.1

## Get genome metadata
xgt genome -k --metadata GCA_001512625.1

# Taxon subcommand: information about a specific taxon
## Get direct descendant of a taxon
xgt taxon g__Escherichia

## Search for a taxon in GTDB's current release
xgt taxon -kw --search g__Escherichia

## Search for a taxon in GTDB's current release with partial matching
xgt taxon -k --search g__Escherichia

⚠️ Issue Tracker

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.

⚖️ License

xgt is distributed under the terms of both the MIT license and the Apache License (Version 2.0).

See LICENSE-APACHE and LICENSE-MIT for details.

Full help is available from xgt --help.

Minimum supported Rust version

xgt minimum Rust version is 1.70.0.

Semver

xgt is following Semantic Versioning 2.0.

Note

Unstable work is on dev branch.