使用纳米孔长读数和NanoMethPhase的百万级甲基化分相。

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2021-02-22 DOI:10.1186/s13059-021-02283-5
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A Marra, Martin Hirst, Steven J M Jones
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引用次数: 25

摘要

纳米孔测序在产生长读段的同时检测修饰核苷酸的能力使其成为检测和分阶段等位基因特异性甲基化的理想选择。然而,目前还没有完整的软件来检测snp,分相单倍型,并从纳米孔序列数据中定位甲基化。在这里,我们提出NanoMethPhase,一个软件工具,从纳米孔测序相5-甲基胞嘧啶。我们还提出了SNVoter,它可以对纳米孔SNV呼叫进行后处理,以提高低覆盖区域的准确性。总之,这些工具可以使用纳米孔序列数据准确地检测等位基因特异性甲基化,并且具有大约10倍冗余的低覆盖率。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase.

The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no complete software for detecting SNPs, phasing haplotypes, and mapping methylation to these from nanopore sequence data. Here, we present NanoMethPhase, a software tool to phase 5-methylcytosine from nanopore sequencing. We also present SNVoter, which can post-process nanopore SNV calls to improve accuracy in low coverage regions. Together, these tools can accurately detect allele-specific methylation genome-wide using nanopore sequence data with low coverage of about ten-fold redundancy.

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来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
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