UBC Faculty Research and Publications

Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase Akbari, Vahid; Garant, Jean-Michel; O’Neill, Kieran; Pandoh, Pawan; Moore, Richard; Marra, Marco A.; 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.

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Attribution 4.0 International (CC BY 4.0)

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