ID | 65773 |
フルテキストURL | |
著者 |
Furuta, Tomoyuki
Institute of Plant Science and Resources, Okayama University
Ashikari, Motoyuki
Bioscience and Biotechnology Center, Nagoya University
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抄録 | Reduced-representation sequencing (RRS) provides cost-effective and time-saving genotyping platforms. Despite the outstanding advantage of RRS in throughput, the obtained genotype data usually contain a large number of errors. Several error correction methods employing the hidden Markov model (HMM) have been developed to overcome these issues. These methods assume that markers have a uniform error rate with no bias in the allele read ratio. However, bias does occur because of uneven amplification of genomic fragments and read mismapping. In this paper, we introduce an error correction tool, GBScleanR, which enables robust and precise error correction for noisy RRS-based genotype data by incorporating marker-specific error rates into the HMM. The results indicate that GBScleanR improves the accuracy by more than 25 percentage points at maximum compared to the existing tools in simulation data sets and achieves the most reliable genotype estimation in real data even with error-prone markers.
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キーワード | reduced-representation sequencing
error correction
imputation
hidden Markov model
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発行日 | 2023-03-29
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出版物タイトル |
Genetics
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巻 | 224巻
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号 | 2号
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出版者 | Oxford University Press (OUP)
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開始ページ | iyad055
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ISSN | 1943-2631
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資料タイプ |
学術雑誌論文
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言語 |
英語
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OAI-PMH Set |
岡山大学
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著作権者 | © The Author(s) 2023.
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論文のバージョン | publisher
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PubMed ID | |
DOI | |
Web of Science KeyUT | |
関連URL | isVersionOf https://doi.org/10.1093/genetics/iyad055
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ライセンス | https://creativecommons.org/licenses/by/4.0/
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Citation | Tomoyuki Furuta and others, GBScleanR: robust genotyping error correction using a hidden Markov model with error pattern recognition, Genetics, Volume 224, Issue 2, June 2023, iyad055, https://doi.org/10.1093/genetics/iyad055
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助成機関名 |
Japan Science and Technology Agency
Japan International Cooperation Agency
Ministry of Education, Culture, Sports, Science and Technology
Japan Society for the Promotion of Science
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助成番号 | JPMJCR13B1
JPMJSA1706
JP20H05912
JP20K15503
JP20H02958
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