|Read mapping and read compression on de Bruijn graphs|
du groupe BioInformatique et Visualisation
|Date|| 2015-05-28 11:00-12:00|
|Titre||Read mapping and read compression on de Bruijn graphs |
|Résumé||1st 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.
|Lieu||salle 178, LaBRI |
|Orateur||Pierre Peterlongo et Guillaume Rizk |
|Url||INRIA Rennes |
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