Section: New Results

Parallelism

Variant detection using processing-in-memory technology

Participants : Charles Deltel, Dominique Lavenier.

The concept of Processing-In-Memory aims to dispatch the computer power near the data. Together with the UPMEM company (http://www.upmem.com/), which is currently developing a DRAM memory enhanced with computing units, we investigate the parallelization of the detection of mutations on the human genome. Traditionnaly, this process is split into 2 steps: a mapping step and a variant calling step. Here, thanks to the high processing power of this new type of memory, the mapping step can nearly be done at the disk transfer rate, allowing the variant calling step to be done simultaneously on the host processor. The implementation is currently on going. First performance evaluations indicate speed-up of one or two order of magnitude compared to purely software implementation.