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

BMC Genomics
Jeremie S KimOnur Mutlu

Abstract

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. 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 m...Continue Reading

References

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Citations

Mar 30, 2019·Bioinformatics·Mohammed AlserCan Alkan
May 22, 2021·BMC Bioinformatics·Yiqing YanRaja Appuswamy
May 27, 2021·Bioinformatics·Tony RobinsonPriyank Shukla
Jul 28, 2021·Bioinformatics·Peter PerešíniTomáš Vinař
Aug 28, 2021·Genome Biology·Mohammed AlserSerghei Mangul
Mar 22, 2018··Allan KniesAki Kuusela
Nov 6, 2019··Jiwon ChoeR. Iris Bahar
Jun 18, 2019··Tali MoreshetR. Iris Bahar
May 23, 2019··Stefano CordaGeraldo F. Oliveira
May 23, 2019··Rachata AusavarungnirunJuan Gómez-Luna
May 4, 2020··Kaizen Vinz A. BorjaRoger Luis Uy
Dec 18, 2020··Ann Franchesca LagunaXunzhao Yin

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Methods Mentioned

BETA
chips
chip

Software Mentioned

GRI
Tibco
Filter Generator
Bowtie
3D
HBM2
GRIM
BWA
mrFAST
- Filter

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