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Introduction

goat-cli is a command line tool with the primary aim of making genome metadata across the tree of life easy to access for all. With few exceptions, all of the output is tab-separated, making it easy to view and manipulate the data for downstream processing or analyses.

GoaT has other user interfaces too. Check out either the website, or the API Docs:

• https://goat.genomehubs.org/
• https://goat.genomehubs.org/api

News

30.06.22

Note that version 0.2.0 has breaking changes from 0.1.55.

• goat-cli search <flags> is now goat-cli taxon search <flags>
• goat-cli count <flags> is now goat-cli taxon count <flags>
• goat-cli lookup <flags> is now goat-cli taxon lookup <flags>
• goat-cli newick <flags> is now goat-cli taxon newick <flags>

This change is to reflect the type of data index being used here (taxon). It follows that there are other data indexes. The only other currently implemented is assembly.

• goat-cli assembly search
• goat-cli assembly count
• goat-cli assembly lookup

These commands return data which is assembly-centric, as opposed to taxon-centric data.

This code refactoring also allows us to add further indexes when we can!

Sections

For installation and getting started - Getting started

For basic exploration of the command line tool - Basics

For more advanced use cases - Advanced

For a tutorial - Tutorial

Acknowledgements

Many thanks to Richard Challis, Sujai Kumar, and Cibele Sotero-Caio, who develop and maintain the GoaT databases, website, and API.

Citation

Manuscript in progress!