R&D in genomics and metagenomics

Since 1st February 2012, a genomics laboratory has been implemented at the Institute. This laboratory is aimed at improving the quality and rapidity of bacterial genomes sequencing and in developing new bioinformatic pipelines to rapidly assemble, annotate and interpret newly sequenced genomes for the main benefit of patients' care (Greub G 2013; Bertelli & Greub 2013). In addition to bacterial genomics, functional genomics (De Barsy et al 2014) and metagenomics are two other major parts of the R&D orientation of this new diagnostic laboratory.

The different projects performed so far mainly were aimed at:

• (i) defining ideal targets for molecular diagnosis (Diene et al 2016);
• (ii) investigating the relatedness of different strains (Bertelli et al 2014; Pillonel et al 2016) and looking for virulence factors (Tagini et al, 2016; Pillonel et al, in press).

Since such a laboratory largely rely on competent bioinformaticians, a master level course entitled “Sequence a genome” has been initiated a few years ago and train each year 12 to 24 new biologists (Bertelli et al 2015).