SummarySequana is a Python-based software dedicated to the development of Next Generation Sequencing (NGS) pipelines. We use the Snakemake (Köster and Rahmann 2012) framework to design our pipelines, which eases the decomposition of pipelines into modular sub-units. We currently have 7 pipelines covering quality control, variant calling, long-reads quality, de-novo and RNA-seq analysis (see https://sequana.readthedocs.io for details). Our pipelines are associated with HTML reports based on JINJA templating and Javascript. The reports are used to store the results of a pipelines but also materials required to reproduce the results. Sequana is also a Python library that provides tools to perform various analysis tasks (e.g., variant call filtering). Some of the library components provide original tools that are also available as standalone applications. For instance a fast taxonomic analysis based on Kraken (Wood and Salzberg 2014) as well as a tool to perform exhaustive coverage analysis (Desvillechabrol et al. 2016) (bottom right panel in the image here below).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. Future worksSequana 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.

AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php.