EHItk: a toolkit for accessing Earth Hologenome Initiative data resources

The Earth Hologenome Initiative (EHI) is generating standardized datasets that jointly capture host genomic and microbial metagenomic-namely hologenomic-information across wild vertebrates. These resources include thousands of shotgun hologenomic datasets and metagenome-assembled genomes (MAGs), accompanied by extensive metadata describing host biology, sampling context, and sequencing procedures. Although these datasets are made publicly available, efficient access to them remains challenging due to the distribution of data across multiple repositories and the complexity of the associated metadata.

We present EHItk, a lightweight Python package and command-line toolkit that enables programmatic discovery and retrieval of EHI datasets and their metadata. EHItk allows users to query hologenomes and MAGs using biologically meaningful metadata filters. The software translates these filters into SQL queries against a local database and supports downloading matched raw FASTQ reads and genome FASTA files. By simplifying metadata-driven dataset discovery and retrieval, EHItk facilitates the integration of EHI resources into bioinformatic pipelines and enables large-scale comparative analyses across hosts and microbial genomes.

EHItk supports Python 3.10 and later. It is distributed as open-source software under the GNU General Public License v3 and is available from PyPI, Bioconda and GitHub: https://github.com/earthhologenome/ehitk.