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The linkage method, a novel approach for SNP detection and haplotype reconstruction from a single diploid individual with next generation sequence data
https://ir.soken.ac.jp/records/4510
https://ir.soken.ac.jp/records/4510c87bbe88-195f-4a09-a0f3-770bb0a3e1e5
| Item type | 学術雑誌論文 / Journal Article(1) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 公開日 | 2014-05-14 | |||||||||||
| タイトル | ||||||||||||
| タイトル | The linkage method, a novel approach for SNP detection and haplotype reconstruction from a single diploid individual with next generation sequence data | |||||||||||
| タイトル | ||||||||||||
| タイトル | The linkage method, a novel approach for SNP detection and haplotype reconstruction from a single diploid individual with next generation sequence data | |||||||||||
| 言語 | en | |||||||||||
| 言語 | ||||||||||||
| 言語 | eng | |||||||||||
| 資源タイプ | ||||||||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||||||||
| 資源タイプ | journal article | |||||||||||
| アクセス権 | ||||||||||||
| アクセス権 | metadata only access | |||||||||||
| アクセス権URI | http://purl.org/coar/access_right/c_14cb | |||||||||||
| 著者 |
SASAKI, Eriko
× SASAKI, Eriko
× SUGINO, Ryuichi P.
× INNAN, Hideki
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| 著者別名 |
印南, 秀樹
× 印南, 秀樹
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| 抄録 | ||||||||||||
| 内容記述タイプ | Abstract | |||||||||||
| 内容記述 | When we sequence a diploid individual, the output actually comprises two genomes: one from the paternal parent and the other from the maternal parent. In this study, we introduce a novel heuristic algorithm for distinguishing single-nucleotide polymorphisms (SNPs) from the two parents and phasing them into haplotypes. The algorithm is unique because it simultaneously performs SNP calling and haplotype phasing. This approach can exploit the linkage information of nearby SNPs, which facilitates the efficient removal of haplotypes that originate from incorrectly mapped short reads. Using simulated data we demonstrated that our approach increased the accuracy of SNP calls. The haplotype reconstruction performance depended largely on the density of SNPs. Using current next-generation sequence technology with a relatively short read length, reasonable performance is expected when this approach is applied to species with an average of five heterozygous sites per 1 kb. The algorithm was implemented as the program “linkSNPs.” | |||||||||||
| 書誌情報 |
Molecular Biology and Evolution en : Molecular Biology and Evolution 巻 30, 号 9, p. 2187-2196, 発行日 2013 |
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| 出版者 | ||||||||||||
| 出版者 | Oxford University Press | |||||||||||
| ISSN | ||||||||||||
| 収録物識別子タイプ | ISSN | |||||||||||
| 収録物識別子 | 07374038 | |||||||||||
| DOI | ||||||||||||
| 識別子タイプ | DOI | |||||||||||
| 関連識別子 | https://doi.org/10.1093/molbev/mst103 | |||||||||||
| 関連名称 | 10.1093/molbev/mst103 | |||||||||||
| 権利 | ||||||||||||
| 権利情報 | © The Author 2013. | |||||||||||
