Shouji: a fast and efficient pre-alignment filter for sequence alignment.

ABSTRACT: MOTIVATION:The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability 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. 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 that adopts modern fie

SUBMITTER: Alser M 

PROVIDER: S-EPMC6821304 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature