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

Kim, Jeremie S.; Senol Cali, Damla; Xin, Hongyi; Lee, Donghyuk; Ghose, Saugata; Alser, Mohammed; Hassan, Hasan; Ergin, Oğuz; Alkan, Can; Mutlu, Onur (BioMed Central Ltd., 2018-05-09)
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. ...
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GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping 

Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oğuz; Mutlu, Onur; Alkan, Can (Oxford Univ Press, 2017-11-01)
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments - called short reads- that cause significant computational burden. To analyze the entire genome, each of the ...

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AuthorAlkan, Can (2)Alser, Mohammed (2)Ergin, Oğuz (2)Hassan, Hasan (2)Mutlu, Onur (2)
Xin, Hongyi (2)
Ghose, Saugata (1)Kim, Jeremie S. (1)Lee, Donghyuk (1)Senol Cali, Damla (1)Subject3D-stacked DRAM (1)Emerging memory technologies (1)Exome (1)Genome (1)Genome sequencing (1)High throughput sequencing (1)Processing-in-memory (1)read mapping (1)Seed location filtering (1)... View MoreDate Issued2017 (1)2018 (1)Has File(s)No (1)Yes (1)Typearticle (2)CoverageMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı (2)WOSWOS:000413645800004 (1)WOS:000431831100003 (1)Scopus2-s2.0-85034098310 (1)2-s2.0-85045409488 (1)PubMedPMID:28575161 (1)PMID:29764378 (1)Avrupa Birliği Destekli Yayın SayısıMarie Curie Career Integration Grant [PCIG-2011-303772] (1)TÜBİTAK Destekli Yayın SayısıScientific and Technological Research Council of Turkey, under the TUBITAK 2215 program (1)Dileng (2)Erişiminfo:eu-repo/semantics/openAccess (2)

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