Sequana is an open source project (https://github.com/sequana/sequana). It is developed with the aim of simplifying the development of new tools (for developers) and the deployment of the pipelines (for users). The extended documentation (http://sequana.readthedocs.org) and test suite (on Travis.org) provide a high-quality software that is routinely tested. Sequana is now available on bioconda making the installation easier and faster by taking care of the dependencies (e.g., samtools, bwa, or Python libraries).
Finally, for end-users, we also developed a Graphical interface called Sequanix (Desvillechabrol et al. 2017) developed with the PyQt framework (see left panel of the image here below). Sequanix standalone exposes all Sequana pipelines (Snakemake pipelines) within an easy-to-use interface. Within the graphical interface, the configuration file used by Snakemake are automatically loaded and can be edited by end-users with dedicated widgets. We made the interface generic enough that not only Sequana pipelines can be run interactively but also any Snakemake pipelines.
Sequana is an on-going project. Although the project has reached a mature stage with stable pipelines, new pipelines will be including on demand or based on new technologies.
Desvillechabrol, Dimitri, Christiane Bouchier, Sean Kennedy, and Thomas Cokelaer. 2016. “Detection and Characterization of Low and High Genome Coverage Regions Using an Efficient Running Median and a Double Threshold Approach.” bioRxiv. doi:https://doi.org/10.1101/092478.
Desvillechabrol, Dimitri, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, and Thomas Cokelaer. 2017. “Sequanix: A Dynamic Graphical Interface for Snakemake Workflows.” bioRxiv. doi:https://doi.org/10.1101/162701.
Köster, Johannes, and Sven Rahmann. 2012. “Snakemake - a Scalable Bioinformatics Workflow Engine.” Bioinformatics 28 (19). Oxford University Press: 2520–2.
Wood, Derrick E., and Steven L. Salzberg. 2014. “Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments.” Genome Biology 15:R46.