NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing.

Yang Liu¹, Hash Brown Taha¹, Qiuyang Zhang¹, Ziwei Pan^2,3, Christina Chatzipantsiou⁴, Emma Wade⁵, Thatcher Slocum², Lasya Karuturi², Yue Zhao², Shilpita Karmakar², Sheng Li¹

¹Department of Cancer Biology, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.

²The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.

³Department of Genetics and Genome Sciences, UConn Health Center, Farmington, CT, USA.

⁴Lifebit Biotech Ltd., London, UK.

⁵Department of Computer Science and Engineering, Mississippi State University, Starkville, MS.

PubMed PMC DOI PDF

Abstract

Nanopore long-read sequencing has expanded the capacity of long-range, single-base, and single-molecule DNA-methylation (DNAme) detection and haplotype-aware allele-specific epigenetic phasing. Previously, we benchmarked and ranked the robustness of seven computational tools for DNAme detection using nanopore sequencing. The top performers were Megalodon, Nanopolish, DeepSignal and Guppy. However,…

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