EHItk documentation

The Earth Hologenome Initiative ToolKit (EHItk) is a Python package and command-line tool for finding, summarizing, exporting, and downloading EHI specimen, hologenome, and metagenome-assembled genome (MAG) records.

EHItk is organized around three data levels:

  • specimens for host and specimen metadata.

  • hologenomes for shotgun metagenomic sequencing datasets.

  • mags for metagenome-assembled genomes linked to parent hologenomes.

Each level uses the same action pattern where possible: query returns matching records, values counts distinct field values, stats summarizes matching records, and fetch downloads files for hologenomes and MAGs.

EHItk includes a pytest-based unit test suite in the repository’s tests/ directory. The project is also covered by GitHub Actions continuous integration, which runs the tests, builds source and wheel distributions, and performs CLI smoke tests across supported Python versions.

Quick example

ehitk specimens query --host-species "Podarcis muralis" --limit 5
ehitk hologenomes query --host-lineage Reptilia --columns hologenome_id,host_species,data_gb
ehitk mags stats --quality high --species "Escherichia coli"

Contents