Allele-specific methylation detection using nanopore sequencing and NanoMethPhase
About Vahid Akbari
Vahid Akbari is a Ph.D. student in Medical Genetics at the University of British Columbia, and a research assistant at the Canada's Michael Smith Genome Sciences Centre in Vancouver. He is particularly interested in epigenome and epigenetic modifications happening on DNA and is using nanopore sequencing to study epigenetic alterations contributing in human cancer development.
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 a workflow and NanoMethPhase, a 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 coverage as low as ten-fold redundancy.