Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase

被引：42

作者：

Akbari, Vahid ^{[1
,2
]}

Garant, Jean-Michel ^{[1
]}

O'Neill, Kieran ^{[1
]}

Pandoh, Pawan ^{[1
]}

Moore, Richard ^{[1
]}

Marra, Marco A. ^{[1
,2
]}

Hirst, Martin ^{[1
,3
]}

Jones, Steven J. M. ^{[1
,2
]}

机构：

[1] BC Canc, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC, Canada

[2] Univ British Columbia, Dept Med Genet, Vancouver, BC, Canada

[3] Univ British Columbia, Dept Microbiol & Immunol, Michael Smith Labs, Vancouver, BC, Canada

来源：

GENOME BIOLOGY | 2021年 / 22卷 / 01期

关键词：

Nanopore sequencing; Allele-specific methylation; Phasing; NanoMethPhase; DNA METHYLATION; MONOALLELIC EXPRESSION; BASE MODIFICATIONS; IMPRINTED GENES; NEURAL-NETWORK; GENOME; INACTIVATION; REVEALS; TOOL;

D O I：

10.1186/s13059-021-02283-5

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：21

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