Eliminating heterozygosity from reads through coverage normalization
Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review
Author(s)
Related Research Unit(s)
Detail(s)
| Original language | English |
|---|---|
| Title of host publication | Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 |
| Editors | T Tian, Q Jiang, Y Liu, K Burrage, J Song, Y Wang, Hu, S Morishita, Q Zhu, G Wang |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. |
| Pages | 174-177 |
| ISBN (print) | 9781509016105 |
| Publication status | Published - 17 Jan 2017 |
Publication series
| Name | IEEE International Conference on Bioinformatics and Biomedicine-BIBM |
|---|---|
| Publisher | IEEE COMPUTER SOC |
| ISSN (Print) | 2156-1125 |
Conference
| Title | 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 |
|---|---|
| Place | China |
| City | Shenzhen |
| Period | 15 - 18 December 2016 |
Link(s)
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 et al.
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).
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 32 - Refereed conference paper (with host publication) › peer-review
