Variant Calling Parallelization on Processor-in-Memory Architecture [article]

Dominique LAVENIER, Romaric Jodin, Remy Cimadomo
2020 biorxiv/medrxiv   pre-print
In this paper, we introduce a new combination of software and hardware PIM (Process-in-Memory) architecture to accelerate the variant calling genomic process. PIM translates into bringing data intensive calculations directly where the data is: within the DRAM, enhanced with thousands of processing units. The energy consumption, in large part due to data movement, is significantly lowered at a marginal additional hardware cost. Such design allows an unprecedented level of parallelism to process
more » ... illions of short reads. Experiments on real PIM devices developed by the UPMEM company show significant speed-up compared to pure software implementation. The PIM solution also compared nicely to FPGA or GPU based acceleration bringing similar to twice the processing speed but most importantly being 5 to 8 times cheaper to deploy with up to 6 times less power consumption.
doi:10.1101/2020.11.03.366237 fatcat:e4vid6ixr5h25dnutnhtvkxxzm