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Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase Akbari, Vahid; Garant, Jean-Michel; O’Neill, Kieran; Pandoh, Pawan; Moore, Richard; Marra, Marco, 1966-; Hirst, Martin; Jones, Steven J. M.

Abstract

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.

Item Metadata

Title
Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
Creator
Akbari, Vahid; Garant, Jean-Michel; O’Neill, Kieran; Pandoh, Pawan; Moore, Richard; Marra, Marco, 1966-; Hirst, Martin; Jones, Steven J. M.
Contributor
Michael Smith Laboratories
Publisher
BioMed Central
Date Issued
2021-02-22
Description
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.
Subject
Nanopore sequencing; Allele-specific methylation; Phasing; NanoMethPhase
Genre
Article
Type
Text
Language
eng
Date Available
2021-02-24
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0395957
URI
http://hdl.handle.net/2429/77374
Affiliation
Medicine, Faculty of; Science, Faculty of; Other UBC; Non UBC; Medical Genetics, Department of; Microbiology and Immunology, Department of
Citation
Genome Biology. 2021 Feb 22;22(1):68
Publisher DOI
10.1186/s13059-021-02283-5
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
The Author(s)
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)