isiteuk
isiteuk classifies genomes by domain (Bacteria, Archaea, Eukaryota) using SingleM marker genes.
Installation
Conda (recommended)
conda create -c conda-forge -c bioconda --override-channels --name isiteuk isiteuk
conda activate isiteuk
PyPI
pip install isiteuk
Non-Python dependencies (SingleM, DIAMOND) must be installed separately — see pixi.toml for the full list.
GitHub (development)
git clone https://github.com/wwood/isiteuk
cd isiteuk
pixi shell
isiteuk --help
This installs isiteuk and all dependencies (including SingleM) into a managed environment via pixi.
Reference data
Download the isiteuk metapackage from Zenodo:
isiteuk data --output-directory /path/to/isiteuk-data
export ISITEUK_METAPACKAGE_PATH=/path/to/isiteuk-data/isiteuk-backpack-0.0.1
Add the export line to your .bashrc or equivalent to avoid repeating it. To verify the download:
isiteuk data --verify-only
Usage
Classify genomes
isiteuk process \
--output results.tsv \
--genome-list genomes.txt \
--threads 64
Or pass genomes directly:
isiteuk process \
--output results.tsv \
--genomes genome1.fna.gz genome2.fna.gz \
--threads 64
The --metapackage flag can override ISITEUK_METAPACKAGE_PATH for a one-off run:
isiteuk process \
--metapackage /path/to/isiteuk-0.0.1.smpkg \
--output results.tsv \
--genomes genome1.fna.gz
To resume an interrupted run:
isiteuk process --continue \
--output results.tsv \
--genome-list genomes.txt
Output format
Tab-separated file with one row per genome per domain detected:
| genome | domain | num_in_target_domain | num_not_in_target_domain |
|---|---|---|---|
| genome1 | d__Bacteria | 14.2 | 0.0 |
| genome2 | d__Eukaryota | 8.7 | 1.3 |
Running tests
Quick tests (no metapackage required):
pixi run test
Full integration tests (requires ISITEUK_METAPACKAGE_PATH to be set):
pixi run test-expensive
Run a single test by name:
pixi run run-a-test test_bacterial_genome
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