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dc.contributor.authorKim, Jeremie S.
dc.contributor.authorSenol Cali, Damla
dc.contributor.authorXin, Hongyi
dc.contributor.authorLee, Donghyuk
dc.contributor.authorGhose, Saugata
dc.contributor.authorAlser, Mohammed
dc.contributor.authorHassan, Hasan
dc.contributor.authorErgin, Oğuz
dc.contributor.authorAlkan, Can
dc.contributor.authorMutlu, Onur
dc.date.accessioned2019-03-14T18:33:44Z
dc.date.available2019-03-14T18:33:44Z
dc.date.issued2018-05-09
dc.identifier.citationKim, J. S., Cali, D. S., Xin, H., Lee, D., Ghose, S., Alser, M., ... & Mutlu, O. (2018). GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC genomics, 19(2), 89.
dc.identifier.urihttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4460-0
dc.identifier.urihttp://hdl.handle.net/20.500.11851/709
dc.description.abstractBackground: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i.e., sequence alignment) to determine the origin of the read. A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments. Results: We propose a novel seed location filtering algorithm, GRIM-Filter, optimized to exploit 3D-stacked memory systems that integrate computation within a logic layer stacked under memory layers, to perform processing-in-memory (PIM). GRIM-Filter quickly filters seed locations by 1) introducing a new representation of coarse-grained segments of the reference genome, and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for a sequence alignment error tolerance of 0.05, GRIM-Filter 1) reduces the false negative rate of filtering by 5.59x-6.41x, and 2) provides an end-to-end read mapper speedup of 1.81x-3.65x, compared to a state-of-the-art read mapper employing the best previous seed location filtering algorithm. Conclusion: GRIM-Filter exploits 3D-stacked memory, which enables the efficient use of processing-in-memory, to overcome the memory bandwidth bottleneck in seed location filtering. We show that GRIM-Filter significantly improves the performance of a state-of-the-art read mapper. GRIM-Filter is a universal seed location filter that can be applied to any read mapper. We hope that our results provide inspiration for new works to design other bioinformatics algorithms that take advantage of emerging technologies and new processing paradigms, such as processing-in-memory using 3D-stacked memory devices.en_US
dc.description.sponsorshipSRC ; NIH [HG006004]
dc.language.isoeng
dc.publisherBioMed Central Ltd.en_US
dc.relation.isversionof10.1186/s12864-018-4460-0
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectHigh throughput sequencingen_US
dc.subjectGenome sequencingen_US
dc.subjectSeed location filteringen_US
dc.subject3D-stacked DRAMen_US
dc.subjectProcessing-in-memoryen_US
dc.subjectEmerging memory technologiesen_US
dc.titleGRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologiesen_US
dc.typearticle
dc.relation.journalBMC Genomicsen_US
dc.contributor.departmentTOBB ETÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümütr_TR
dc.contributor.departmentTOBB ETU, Faculty of Engineering, Department of Computer Engineeringen_US
dc.identifier.volume19
dc.identifier.issue2
dc.identifier.startpage89
dc.contributor.orcidErgin, Oğuz [0000-0003-0784-83]
dc.identifier.wosWOS:000431831100003
dc.identifier.scopus2-s2.0-85045409488
dc.contributor.tobbetuauthorErgin, Oğuz
dc.contributor.YOKid143001
dc.identifier.PubMedIDPMID:29764378
dc.identifier.doi10.1186/s12864-018-4460-0
dc.contributor.wosresearcherIDErgin, Oğuz [E-5717-2010]
dc.contributor.ScopusAuthorID6603141208
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı


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