funannotate2: eukaryotic genome annotation pipeline

Funannotate2 is a comprehensive eukaryotic genome annotation pipeline that provides a complete workflow for annotating eukaryotic genomes. It integrates various tools and databases to produce high-quality gene predictions and functional annotations.

Quick start: Installation

Linux systems

Unit this gets pushed to bioconda, can try this: shell mamba create -n funannotate2 gfftk gapmm2 minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn gb-io buscolite conda activate funannotate2 python -m pip install git+https://github.com/nextgenusfs/funannotate2.git

Apple Silicon (M series)

Installation on apple silicon (M series) is a little bit more involved due to some dependency issues and non-native builds of some software. I've not been able to find or build a version of augustus that will run, so instead I've been running augustus and genemark locally with Docker. I've setup two repos with instructions on how to get this working (Need Docker Desktop installed) and then will need to put the bash wrapper files in your PATH to mimic the CLI interface.

https://github.com/nextgenusfs/dockerized-augustus

https://github.com/nextgenusfs/dockerized-genemark

Once that is working, you can then install most of the remaining dependencies with conda, although we need to leave out both buscolite and funannotate2 because they have augustus as a dependency, instead we will install those python packages with pip. The conda mkl<2022 is to avoid an annoying warning on apple silicon with the intel mkl package.

```shell

first install most of the dependencies

mamba create -n funannotate2 --platform osx-64 "python>=3.7,<3.13" gfftk gapmm2 minimap2 miniprot snap glimmerhmm diamond trnascan-se gb-io pyhmmer pyfastx requests json-repair pytantan "mkl<2022"

we can then add the required FUNANNOTATE2_DB env variable to the conda environment, note need to reactivate to use it

conda activate funannotate2 conda env config vars set FUNANNOTATE2DB=/path/to/funannotate2-db conda env config vars set AUGUSTUSCONFIG_PATH=/path/to/augustus-3.5.0/config conda deactivate

now reactivate environment, and install the remaining python dependencies with pip

conda activate funannotate2 python -m pip install buscolite git+https://github.com/nextgenusfs/funannotate2.git

now we can install the databases

funannotate2 install -d all ```

Other/Manual Installation

Additional tools like genemarkHMM must be installed manually due to licensing.

funannotate2 is a python package, to install release versions use the pip package manager, like so:

shell pip install funannotate2 Or to install the bleeding edge version from github repo:

shell python -m pip install git+https://github.com/nextgenusfs/funannotate2.git

Development

Testing

Funannotate2 includes both unit tests and integration tests to ensure the code works correctly.

Running Tests

To run the tests, you need to install pytest and the package in development mode:

```bash

Install pytest and coverage tools

pip install pytest pytest-cov

Install funannotate2 in development mode

pip install -e .

Run all tests

pytest

Run with coverage report

pytest --cov=funannotate2

Generate HTML coverage report

python scripts/run_coverage.py ```

For more information about testing, see the TESTING.md file.

Development Dependencies

To work on funannotate2 development, you'll need to install the development dependencies:

shell pip install pytest pytest-cov

Documentation

Funannotate2 includes comprehensive documentation that covers installation, usage, API reference, and more. To build the documentation:

```bash

Install Sphinx and the theme

pip install sphinx sphinxrtdtheme

Build the documentation

cd docs make html ```

The built documentation will be in the docs/_build/html directory.

For more information about the documentation, see the docs/README.md file.

Running Tests

After installing the development dependencies, you can run the tests with:

shell python -m pytest

To run tests with coverage reporting:

shell python -m pytest --cov=funannotate2 --cov-report=term-missing

Or use the provided script to generate an HTML coverage report:

shell python scripts/run_coverage.py

To install the most up to date code from this repo, you can run: python -m pip install git+https://github.com/nextgenusfs/funannotate2.git --upgrade --force --no-deps

Citation

Funannotate2 includes a CITATION.cff file that provides citation information for the software. The version and release date in this file are automatically updated when a new release is created.

To cite funannotate2 in your work, you can use the citation information from the CITATION.cff file or generate a citation in your preferred format using tools like citeas.org.