Titre du projet: 
Assembly for 3rd generation sequencing reads
Porteur: 
RIVALS Eric
Mots clefs: 
Genomics
Long reads
NGS
hybrid assembly
HPC
Description: 

The analysis of deep sequencing data is both a bottleneck and a major issue for life sciences. Deep seq is commonly used to study a variety of genomic mechanisms as different as structural variations or fitness contribution of genes among many others. Sequencing technologies are evolving fast and the third generation is now accessible on the market. Third generation sequencing provides longer reads at the expense of higher error rates that makes them difficult to incorporate in a classical analysis pipeline. Their length carries the promise of overcoming two major problems in genome and transcriptome assembly: the presence of i/ long gemonic repeats and ii/ of distinct alleles in doploid or polyploid genomes. We propose to set up a service to perform de novo genomic and transcriptome assembly of third generation reads eventually combined with accurate second generation reads. This service will be developed, evualated and evoled as both the technique and bioinformatics solutions improved. Long read sequencing will be increasingly used in assembly projects, but to our knowledge no such service is available in an academic environment. Our group has acquired some expertise of error correction of third generation reads (see LoRDEC) and aims at exploiting high performance computing devices for this assembly service.

cea
cnrs
inra
inria
inserm
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