Browsing by Subject "Algorithm/hardware co-design"

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    SeGraM: A universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping
    (Association for Computing Machinery, 2020-06-11) Cali, D.Ş; Kanellopoulos, K.; Lindegger, J.; Bingöl, Zülal; Kalsi, G.S.; Zuo, Z.; Fırtına, Can; Cavlak, M.B.; Kim, J.; Ghiasi, N.M.; Singh, G.; Gómez-Luna, J.; Almadhoun Alserr, N.; Alser, M.; Subramoney, S.; Alkan, Can; Ghose, S.; Mutlu, O.
    A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the linear reference sequence with a graph-based representation of the reference genome, which captures the genetic variations and diversity across many individuals in a population. Mapping reads to the graph-based reference genome (i.e., sequence-to-graph mapping) results in notable quality improvements in genome analysis. Unfortunately, while sequence-to-sequence mapping is well studied with many available tools and accelerators, sequence-to-graph mapping is a more difficult computational problem, with a much smaller number of practical software tools currently available. We analyze two state-of-the-art sequence-to-graph mapping tools and reveal four key issues. We find that there is a pressing need to have a specialized, high-performance, scalable, and low-cost algorithm/hardware co-design that alleviates bottlenecks in both the seeding and alignment steps of sequence-to-graph mapping. Since sequence-to-sequence mapping can be treated as a special case of sequence-to-graph mapping, we aim to design an accelerator that is efficient for both linear and graph-based read mapping. To this end, we propose SeGraM, a universal algorithm/hardware co-designed genomic mapping accelerator that can effectively and efficiently support both sequence-to-graph mapping and sequence-to-sequence mapping, for both short and long reads. To our knowledge, SeGraM is the first algorithm/hardware co-design for accelerating sequence-to-graph mapping. SeGraM consists of two main components: (1) MinSeed, the first minimizer-based seeding accelerator, which finds the candidate locations in a given genome graph; and (2) BitAlign, the first bitvector-based sequence-to-graph alignment accelerator, which performs alignment between a given read and the subgraph identified by MinSeed. We couple SeGraM with high-bandwidth memory to exploit low latency and highly-parallel memory access, which alleviates the memory bottleneck. We demonstrate that SeGraM provides significant improvements for multiple steps of the sequence-to-graph (i.e., S2G) and sequence-to-sequence (i.e., S2S) mapping pipelines. First, SeGraM outperforms state-of-the-art S2G mapping tools by 5.9×/3.9× and 106×/- 742× for long and short reads, respectively, while reducing power consumption by 4.1×/4.4× and 3.0×/3.2×. Second, BitAlign outperforms a state-of-the-art S2G alignment tool by 41×-539× and three S2S alignment accelerators by 1.2×-4.8×. We conclude that SeGraM is a high-performance and low-cost universal genomics mapping accelerator that efficiently supports both sequence-to-graph and sequence-to-sequence mapping pipelines.