EEfinder
EEfinder is a tool/python package that automatizes several tasks related to identification of Endogenous Elements present on Eukaryotic Genomes.
Install
EEfinder drives BLAST, DIAMOND and bedtools, which are not pip-installable — install them first, then the package.
From PyPI
conda create -n EEfinder -c conda-forge -c bioconda \
"python>=3.9,<3.12" "blast>=2.5" "diamond>=2.0.15" "bedtools>=2.27"
conda activate EEfinder
pip install eefinder
From source
Cloning also gives you env.yml, which pins the exact versions EEfinder was developed and tested against (BLAST 2.5.0, DIAMOND 2.0.15, bedtools 2.27.1), plus the example data in test_files/.
git clone https://github.com/WallauBioinfo/EEfinder.git
cd EEfinder
conda env create -f env.yml
conda activate EEfinder
pip install .
Check tool
eefinder --version
#eefinder, version 1.1.2
Documentation
Full documentation is hosted on Read the Docs: https://eefinder.readthedocs.io
Cite us
If you use EEfinder in your research, please cite https://www.sciencedirect.com/science/article/pii/S2001037024003325:
Dias, Y. J. M., Dezordi, F. Z., & Wallau, G. L. (2024). EEFinder: A general-purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes. Computational and Structural Biotechnology Journal. https://doi.org/10.1016/j.csbj.2024.10.012
1 maintainer
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