GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies-Reference-Cited by-同舟云学术

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

Published:2018-05 Issue:S2 Volume:19 Page:
ISSN:1471-2164
Container-title:BMC Genomics
language:en
Short-container-title:BMC Genomics

Author:

Kim Jeremie S.,Senol Cali Damla,Xin Hongyi,Lee Donghyuk,Ghose Saugata,Alser Mohammed,Hassan Hasan,Ergin Oguz,Alkan Can,Mutlu Onur

Publisher

Springer Science and Business Media LLC

Subject

Genetics,Biotechnology

Link

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

Reference104 articles.

1. Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res. 2014; 42.W1:W494–W500.

2. Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X. Hobbes: Optimized Gram-Based Methods for Efficient Read Alignment. Nucleic Acids Res. 2012; 40(6):e41–e41.

3. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, et al. Personalized Copy Number and Segmental Duplication Maps Using Next-Generation Sequencing. Nat Genet. 2009; 41(10):1061–7.

4. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. 2009; 5.5:e1000386.

5. Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C. Sensitive and Fast Mapping of Di-Base Encoded Reads. Bioinformatics. 2011; 27(14):1915–21.

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