公开(公告)号：US20200265923A1

公开(公告)日：2020-08-20

申请号：US16749139

申请日：2020-01-22

Applicant: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

Inventor： Arun SUBRAMANIYAN ,  Satish NARAYANASAMY ,  Reetuparna DAS ,  David T. BLAAUW

IPC: G16B30/10 ,  G06F16/22

Abstract: Read alignment is a time-consuming step in genome sequencing analysis. The most widely used software for read alignment, BWA-MEM and BWA-MEM2 are based on the seed-and-extend paradigm for read alignment. The seeding step of read alignment is a major bottleneck contributing ˜38% of the overall execution time in BWA-MEM2 when aligning whole human genome. This is because BWA-MEM2 uses a compressed index structure called the FMD-Index, which results in high bandwidth requirements, primarily due to its character-by-character processing of reads. To address these challenges, a novel seeding data structure is presented along with a custom accelerator architecture for seeding.