Section: Partnerships and Cooperations

National Initiatives

ANR

• ANR ASTER: ASTER is a national project that aims at developing algorithms and software for analyzing third-generation sequencing data, and more specifically RNA sequencing. Bonsai is the principal investigator in this ANR. Other partners are Erable (LBBE in Lyon) and two sequencing and analysis platforms that have been very active in the MinION Access Program (Genoscope and Institut Pasteur de Lille).

• PIA France Génomique: National funding from “Investissements d'Avenir” (call Infrastructures en Biologie-Santé). France Génomique is a shared infrastructure, whose goal is to support sequencing, genotyping and associated computational analysis, and increases French capacities in genome and bioinformatics data analysis. It gathers 9 sequencing and 8 bioinformatics platforms. Within this consortium, we are responsible for the workpackage devoted to the computational analysis of sRNA-seq data, in coordination with the bioinformatics platform of Génopole Toulouse-Midi-Pyrénées.

ADT

• ADT Vidjil (2015–2017): The purpose of this ADT was to strengthen Vidjil development and to ensure a better diffusion of the software by easing its installation, administration and usability. This enabled the software to be well suited for a daily clinical use. Vidjil is now used in routine practice by seven European hospitals (France, Germany, Italy and Czech Republic). Hospitals from the United Kingdom and the Japan are currently assessing Vidjil and may do their clinical routine practice with the software in a near future.

• ADT SeedLib (2017–2019): The SeedLib ADT aims to consolidate existing software developments in Bonsai, into an existing and well-engineered framework. Bonsai has published several new results on spaced seeds and developed several tools that integrate custom implementations of spaced seeds. In parallel, the GATB project is a C++ software library that facilitates the development of next-generation sequencing analysis tools. It is currently maintained by a collaboration between the GenScale team at Inria Rennes and the Bonsai team. Many users from other institutions (including the Erable team at Inria Rhones-Alpes) actively develop tools using GATB. The core object in GATB is $k$-mers, which can be seen as the predecessor of spaced seeds. The goal of this ADT is to integrate existing space seeds formalisms into GATB, therefore further expanding the features offered by the library, and at the same time provide visibility for tools and results in the Bonsai team.