<![CDATA[BOL: Shouji: a fast and efficient pre-alignment filter for sequence alignment]]> https://bioinformaticsonline.com/bookmarks/view/40217/shouji-a-fast-and-efficient-pre-alignment-filter-for-sequence-alignment? https://bioinformaticsonline.com/bookmarks/view/40217/shouji-a-fast-and-efficient-pre-alignment-filter-for-sequence-alignment Mon, 04 Nov 2019 07:09:45 -0600 https://bioinformaticsonline.com/bookmarks/view/40217/shouji-a-fast-and-efficient-pre-alignment-filter-for-sequence-alignment <![CDATA[Shouji: a fast and efficient pre-alignment filter for sequence alignment]]> The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes.

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We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator design that adopts modern FPGA (field-programmable gate array) architectures to further boost the performance of our algorithm.

More at https://github.com/CMU-SAFARI/Shouji

Address of the bookmark: https://github.com/CMU-SAFARI/Shouji

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