Efficient and fast querying and parsing of GTDB's data

Related tags

Database rust bioinformatics database
Overview

xgt

Continuous Integration codecov

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.

Installation

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

cargo build --release
cargo test
cargo install --path .

Quick start guide

# Search all Aminobacter (genus) genomes
xgt search Aminobacter

# Search all genomes with genus name containing aminobacter
xgt search -p aminobacter

# Search a list of taxon name
xgt search -f list.txt

# Get GTDB genome information
xgt genome GCA_001512625.1

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

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

Full help is available from xgt --help.

Minimum supported Rust version

xgt minimum Rust version is 1.64.0.

Semver

xgt is following Semantic Versioning 2.0.

Licence

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.

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Releases(v0.1.0)
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Anicet Ebou
Bioinformatics.
Anicet Ebou
GitHub
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