Efficient Seeding For Read Alignment
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United States of America Patent
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Issued Date -
Aug 20, 2020
app pub date -
Jan 22, 2020
filing date -
Jan 22, 2019
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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.
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