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

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buir.contributor.authorAlser, Mohammed
buir.contributor.authorMutlu, Onur
buir.contributor.authorAlkan, Can
dc.citation.epage4263en_US
dc.citation.issueNumber21en_US
dc.citation.spage4255en_US
dc.citation.volumeNumber35en_US
dc.contributor.authorAlser, Mohammeden_US
dc.contributor.authorHassan, H.en_US
dc.contributor.authorKumar, A.en_US
dc.contributor.authorMutlu, Onuren_US
dc.contributor.authorAlkan, Canen_US
dc.date.accessioned2020-02-12T08:20:04Z
dc.date.available2020-02-12T08:20:04Z
dc.date.issued2019en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractThe 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 field-programmable gate array (FPGA) architectures to further boost the performance of our algorithm. Shouji significantly improves the accuracy of pre-alignment filtering by up to two orders of magnitude compared to the state-of-the-art pre-alignment filters, GateKeeper and SHD. Our FPGA-based accelerator is up to three orders of magnitude faster than the equivalent CPU implementation of Shouji. Using a single FPGA chip, we benchmark the benefits of integrating Shouji with five state-of-the-art sequence aligners, designed for different computing platforms. The addition of Shouji as a pre-alignment step reduces the execution time of the five state-of-the-art sequence aligners by up to 18.8×. Shouji can be adapted for any bioinformatics pipeline that performs sequence alignment for verification. Unlike most existing methods that aim to accelerate sequence alignment, Shouji does not sacrifice any of the aligner capabilities, as it does not modify or replace the alignment step.en_US
dc.description.provenanceSubmitted by Evrim Ergin (eergin@bilkent.edu.tr) on 2020-02-12T08:20:04Z No. of bitstreams: 1 Shouji_A_fast_and_efficient_pre-alignment_filter_for_sequence_alignment.pdf: 598932 bytes, checksum: a883b0d7f48a0a250c2eab06fb45bfef (MD5)en
dc.description.provenanceMade available in DSpace on 2020-02-12T08:20:04Z (GMT). No. of bitstreams: 1 Shouji_A_fast_and_efficient_pre-alignment_filter_for_sequence_alignment.pdf: 598932 bytes, checksum: a883b0d7f48a0a250c2eab06fb45bfef (MD5) Previous issue date: 2019-11-01en
dc.identifier.doi10.1093/bioinformatics/btz234en_US
dc.identifier.eissnISSN 1460-2059
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/11693/53300
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttps://doi.org/10.1093/bioinformatics/btz234en_US
dc.source.titleBioinformaticsen_US
dc.titleShouji: a fast and efficient pre-alignment filter for sequence alignmenten_US
dc.typeArticleen_US

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