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GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies

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dc.contributor.author Kim, Jeremie S.
dc.contributor.author Senol Cali, Damla
dc.contributor.author Xin, Hongyi
dc.contributor.author Lee, Donghyuk
dc.contributor.author Ghose, Saugata
dc.contributor.author Alser, Mohammed
dc.contributor.author Hassan, Hasan
dc.contributor.author Ergin, Oğuz
dc.contributor.author Alkan, Can
dc.contributor.author Mutlu, Onur
dc.date.accessioned 2019-03-14T18:33:44Z
dc.date.available 2019-03-14T18:33:44Z
dc.date.issued 2018-05-09
dc.identifier.citation Kim, 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.uri https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4460-0
dc.identifier.uri http://hdl.handle.net/20.500.11851/709
dc.description.abstract Background: 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.sponsorship SRC ; NIH [HG006004]
dc.language.iso eng
dc.publisher BioMed Central Ltd. en_US
dc.relation.isversionof 10.1186/s12864-018-4460-0
dc.rights info:eu-repo/semantics/openAccess
dc.subject High throughput sequencing en_US
dc.subject Genome sequencing en_US
dc.subject Seed location filtering en_US
dc.subject 3D-stacked DRAM en_US
dc.subject Processing-in-memory en_US
dc.subject Emerging memory technologies en_US
dc.title GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies en_US
dc.type article
dc.relation.journal BMC Genomics en_US
dc.contributor.department TOBB ETÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü tr_TR
dc.contributor.department TOBB ETU, Faculty of Engineering, Department of Computer Engineering en_US
dc.identifier.volume 19
dc.identifier.issue 2
dc.identifier.startpage 89
dc.contributor.orcid Ergin, Oğuz [0000-0003-0784-83]
dc.identifier.wos WOS:000431831100003
dc.identifier.scopus 2-s2.0-85045409488
dc.contributor.tobbetuauthor Ergin, Oğuz
dc.contributor.YOKid 143001
dc.identifier.PubMedID 29764378
dc.identifier.doi 10.1186/s12864-018-4460-0
dc.contributor.wosresearcherID Ergin, Oğuz [E-5717-2010]
dc.contributor.ScopusAuthorID 6603141208
dc.relation.publicationcategory Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı


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