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Thursday, August 3 • 11:00 - 12:00
Dealing with mass of genomic data. From optimized data structures to advanced memory architectures

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Raw data generated by sequencing machines represent hundreds of Giga bytes of information that are systematically processed to extract useful information. However, this mass of genomic data contains a lot of redundancy that can be captured by optimized data structures, such as the de-Bruijn graph, allowing the full information to fit into a standard computer memory. Alternatively, dedicated memory architectures are another possibility to quickly process this mass of information. The talk will discuss these two alternatives by first presenting an optimized implementation of the de-Bruijn graph and an associated tool box called GATB (Genomic Analysis Tool Box). In the second part, we will introduce the PIM (Processing in Memory) concept and present preliminary results on genomic applications using a PIM chip currently developed by the UPMEM company

avatar for Dominique Lavenier

Dominique Lavenier

Ph.D., Research Director at Centre National de la Recherche Scientifique

Thursday August 3, 2017 11:00 - 12:00
Graduate School of Management Building, room 309 Volkhovskiy Pereulok, 3, St. Petersburg, Russia

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