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Read mapping and read compression on de Bruijn graphs
du groupe BioInformatique et Visualisation

Date 2015-05-28  11:00-12:00
TitreRead mapping and read compression on de Bruijn graphs 
Résumé1st part: Read mapping Mapping reads on references is a central task in numerous genomic studies. Since references are mainly extracted from assembly graphs, it is of high interest to map efficiently on such structures. During this seminar I'll motivate the problem of mapping reads on a de Bruijn graph and I'll present a practical solution and its implementation called BGREAT. BGREAT handles real world instances of the problem with moderate resources, as witnessed by the results that will also be presented. 2nd part: Read compression Data volumes generated by NGS is a major concern. It triggered the need for more efficient methods than general purpose compression tools like gzip. In this seminar I will introduce Leon, a reference-free compression method based on a de Bruijn graph. A 'light' graph is constructed and used as a reference to map and store reads efficiently, the same structure is also used for quality scores compression. I will present the algorithm and comparative results.  
Lieusalle 178, LaBRI 
OrateurPierre Peterlongo et Guillaume Rizk 
UrlINRIA Rennes 

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