Sequanix

Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows.

Python version

3.8, 3.9, 3.10

Documentation

On readthedocs

Issues

On github

How to cite

Citations are important for us to carry on developments.

For Sequanix: Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer. Sequanix: A Dynamic Graphical Interface for Snakemake Workflows Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034 Also available on bioRxiv (DOI: https://doi.org/10.1101/162701)

Sequanix is a derivative of the Sequana project that is dedicated to the analyse of NGS data (sequencing data). We provide a set of NGS pipelines including quality control, variant calling, coverage, taxonomy, transcriptomics. Please see the Sequana documentation for an up-to-date status and further information.

Notes

Fix OpenGL for mac Big Sur: https://stackoverflow.com/a/64021312/11988671

Installation

Please see the installation notes and installation steps on the https://sequana.readthedocs.io link.

In brief:

pip install sequanix

For developers, use:

git clone git@github.com:sequana/sequanix.git
pip install -e .[testing]

More documentation

For now, you may find more documentation on https://sequana.readthedocs.io

Design choice

Uses PySide6 from v0.2.0. See e.g., https://www.pythonguis.com/faq/pyqt6-vs-pyside6/ from information on the switch to PySide6. In brief, the Qt project has recently adopted PySide as the official Qt for Python release which should ensure its viability going forward. When we migrate PyQt5 to PyQt6, we therefore decided to use PySide instead of PyQt.

Changelog

Version	Description
0.3.0	* refactoring to use click and new sequana_pipetools
0.2.0	add logo remove pin on python3.7 switch from PyQt5 to PySide6 remove automatic creation of readtag in config. we let the pipelines handle it
0.1.0	* revamp Sequanix independently of Sequana