Sequana is a versatile tool that provides
- A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).
- A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable rules (see Rules).
- Original tools to help in the creation of such pipelines including HTML reports.
- Standalone applications:
- sequana_coverage ease the extraction of genomic regions of interest and genome coverage information
- sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated databases to be downloaded.
- Sequanix: GUI for snakemake workflows, a GUI for Snakemake workflows (hence Sequana pipelines as well)
Currently, the available pipelines cover quality control (e.g. adapters removal, phix removal, trimming of bad quality bases), variant calling, characterisation of the genome coverage, taxonomic classification, de-novo assembly, RNA-seq. See the Pipelines section for more information.
Sequana can be used by developers to create new pipelines and by users in the form of applications ready for production. Moreover, Sequanix can be used to set the parameters of pipelines and execute them easily with a graphical user interface.
We designed a PyQt graphical user interface – Sequanix – aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (https://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to both Snakemake developers in exposing their pipelines and to a wide audience of users.