Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase

Genome Biol. 2021 Feb 22;22(1):68. doi: 10.1186/s13059-021-02283-5.


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.

Keywords: Allele-specific methylation; NanoMethPhase; Nanopore sequencing; Phasing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Chromosomes, Human, X
  • Computational Biology / methods*
  • DNA Methylation*
  • Epigenomics / methods
  • Gene Frequency
  • Genes, X-Linked
  • Haplotypes
  • Humans
  • Mutation
  • Nanopore Sequencing*
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA
  • Software*
  • X Chromosome Inactivation