De novo assembly of bovine genome using PacBio applications

Background and objectives GeT-PlaGe is a genomic core facility which provides technologies and expertise in genome sequencing to academic and private research teams. The SeqOccIn (Sequencing Occitanie Innovation) project, supported by Get-PlaGe and Genotoul Bioinfo platforms, was selected by the Occitanie Region as part of the call for projects "Regional Research and Innovation Platforms". The main objective is to acquire expertise on the optimal combination of long fragment sequencing technologies and associated applications to better characterize complex genomes in agronomical field: from SNP and structural variations detection, to the production of a high quality assemblies. Therefore, to obtain the best genome using PacBio datas, several de novo assembly strategies on a Charolais bovine will be presented : CLR datas only, CCS datas only and trio binning approach. In this poster, we highlight biologicial and bioinformatic aspects taking into account the scientific purpose and different constraints (time, budget, samples qualities). For this work, we sequenced the same individual (offspring bovine) with different applications: PacBio, ONT and Hi-C, and parents with classical short reads (2x150 pb Illumina).