Name
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). |
Year | DOI | Venue |
|---|---|---|
2016 | 10.1109/BIBM.2016.7822514 | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) |
Keywords | Field | DocType |
heterozygosity,coverage normalization,sophisticated algorithms,Hank,normalized k-mers,heterozygous regions,de novo genome assembly,SOAPdenovo2,ALLPATH-LG,Platanus | Assimilation (phonology),Normalization (statistics),Biology,Genomics,Loss of heterozygosity,Whole genome sequencing,Bioinformatics,Genetics,Sequence assembly | Conference |
ISSN | ISBN | Citations |
2156-1125 | 978-1-5090-1612-9 | 0 |
PageRank | References | Authors |
0.34 | 11 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zicheng Zhao | 1 | 1 | 1.42 |
| Yen Kaow Ng | 2 | 73 | 9.46 |
| Xiaodong Fang | 3 | 0 | 0.34 |
| Shuai Cheng Li | 4 | 184 | 30.25 |