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

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

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 locatio...

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Bibliographic Details
Main Authors: Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
Format: Article
Language:English
Published: BMC 2018-05-01
Series:BMC Genomics
Subjects:
High throughput sequencing
Genome sequencing
Seed location filtering
3D-stacked DRAM
Processing-in-memory
Emerging memory technologies
Online Access:http://link.springer.com/article/10.1186/s12864-018-4460-0

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http://link.springer.com/article/10.1186/s12864-018-4460-0

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