Eliminating heterozygosity from reads through coverage normalization

Research output: Chapters, Conference Papers, Creative and Literary Works (RGC: 12, 32, 41, 45)32_Refereed conference paper (with ISBN/ISSN)peer-review

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Detail(s)

Original languageEnglish
Title of host publicationProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
EditorsT Tian, Q Jiang, Y Liu, K Burrage, J Song, Y Wang, Hu, S Morishita, Q Zhu, G Wang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages174-177
ISBN (Print)9781509016105
Publication statusPublished - 17 Jan 2017

Publication series

NameIEEE International Conference on Bioinformatics and Biomedicine-BIBM
PublisherIEEE COMPUTER SOC
ISSN (Print)2156-1125

Conference

Title2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
PlaceChina
CityShenzhen
Period15 - 18 December 2016

Abstract

Heterozygosity has long plagued genome assembly. A wealth of sophisticated algorithms and procedures have been introduced for their treatment in genome assembly. In this paper, we propose a method called Hank (Heterozygosity assimilation through normalized k-mers) for this purpose. The method eliminates heterozygosity from reads by modifying the k-mers in heterozygous regions to increase their coverages to the levels of those in homozygous regions. When evaluated on simulated Illumina data at levels of heterozygosity from 0.1% to 2.0%, Hank was able to remove 80∼96% of the heterozygosity. We also examined the effects of the corrections on de novo genome assembly using SOAPdenovo2, ALLPATH-LG and Platanus. All three methods improved in performance using the treated k-mers (we do not include these assembly results in this manuscript due to space constraint).

Research Area(s)

  • ERROR-CORRECTION, GENOME SEQUENCE, DRAFT GENOME, ALGORITHMS, REVEALS

Citation Format(s)

Eliminating heterozygosity from reads through coverage normalization. / Zhao, Zicheng; Ng, Yen Kaow; Fang, Xiaodong; Li, Shuaicheng.

Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. ed. / T Tian; Q Jiang; Y Liu; K Burrage; J Song; Y Wang; Hu; S Morishita; Q Zhu; G Wang. Institute of Electrical and Electronics Engineers Inc., 2017. p. 174-177 7822514 (IEEE International Conference on Bioinformatics and Biomedicine-BIBM).

Research output: Chapters, Conference Papers, Creative and Literary Works (RGC: 12, 32, 41, 45)32_Refereed conference paper (with ISBN/ISSN)peer-review