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art-egorov / lovis4u

Bioinformatics tool for Locus Visualisation
Do What The F*ck You Want To Public License
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Description

LoVis4u is a bioinformatics tool for Locus Visualisation.

Supported input: Genbank, gff3 with sequence
Supported output: Static vector graphics (pdf)
Programming language: Python3
OS: MacOS, Linux
Python dependencies: biopython, bcbio-gff, scipy, configs, argparse, pandas, distinctipy, matplotlib, seaborn, reportlab
Python version: >= 3.8
OS-level dependencies: MMseqs2 (included in the package)
License: WTFPL
Version: 0.0.8 (September 2024)

Detailed documentation with user guide is available at LoVis4u Homepage

Pipeline:

Visualisation examples:

Installation

python3 -m pip install lovis4u
git clone https://github.com/art-egorov/lovis4u.git
cd lovis4u
python3 -m pip install --upgrade pip
python3 -m pip install setuptools wheel
python3 setup.py sdist
python3 -m pip install -e .

! If you're a linux user, run lovis4u --linux post-install command once to update paths in the premade config files that set by default for MacOS users.

Reference

If you find LoVis4u useful, please cite:
Artyom. A. Egorov, Gemma C. Atkinson, LoVis4u: Locus Visualisation tool for comparative genomics, bioRxiv 2024.09.11.612399; doi: 10.1101/2024.09.11.612399

Contact

Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
You can also use Discussions section for sharing your ideas or feature requests!

Authors

LoVis4u is developed by Artyom Egorov at the Atkinson Lab, Department of Experimental Medical Science, Lund University, Sweden. We are open for suggestions to extend and improve LoVis4u functionality. Please don't hesitate to share your ideas or feature requests.