Nika Mansouri Ghiasi1, Jisung Park1, Harun Mustafa1, Jeremie Kim1, Ataberk Olgun1, Arvid E. Gollwitzer1, Damla Senol Cali2, Can Firtina1, Haiyu Mao1, Nour Almadhoun Alserr1, Rachata Ausavarungnirun3, Nandita Vijaykumar4, Mohammed Alser1, Onur Mutlu1
1ETH Zürich, 2Bionano Genomics, 3KMUTNB, 4University of Toronto
Read mapping is a fundamental step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome (called a reference genome). Read mapping is costly because it needs to perform approximate string matching (ASM) on large amounts of data. To address the computational challenges in genome analysis, many prior works propose various approaches such as accurate filters that select the reads within a dataset of genomic reads (called a read set) that must undergo expensive computation, efficient heuristics, and hardware acceleration. While effective at reducing the amount of expensive computation, all such approaches still require the costly movement of a large amount of data from storage to the rest of the system, which can significantly lower the end-to-end performance of read mapping in conventional and emerging genomics systems. We propose GenStore, the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. GenStore leverages hardware/software co-design to address the challenges of in-storage processing, supporting reads with 1) different properties such as read lengths and error rates, which highly depend on the sequencing technology, and 2) different degrees of genetic variation compared to the reference genome, which highly depends on the genomes that are being compared. Through rigorous analysis of read mapping processes of reads with different properties and degrees of genetic variation, we meticulously design low-cost hardware accelerators and data/computation flows inside a NAND flashbased solid-state drive (SSD). Our evaluation using a wide range of real genomic datasets shows that GenStore, when implemented in three modern NAND flash-based SSDs, significantly improves the read mapping performance of state-of-the-art software (hardware) baselines by 2.07-6.05× (1.52-3.32×) for read sets with high similarity to the reference genome and 1.45-33.63× (2.70-19.2×) for read sets with low similarity to the reference genome.
https://doi.org/10.1145/3503222.3507702