Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering

Abstract

The advent of long-read sequencing methods provides new opportunities for profiling the epigenome - especially as the methylation signature comes for "free" when native DNA is sequenced on either Oxford Nanopore or Pacific Biosciences instruments. However, we lack tools to visualize and analyze data generated from these new sources. Recent efforts from the GA4GH consortium have standardized methods to encode modification location and probabilities in the BAM format. Leveraging this standard format, we developed a technology-agnostic tool, modbamtools to visualize, manipulate and compare base modification/methylation data in a fast and robust way. modbamtools can produce high quality, interactive, and publication-ready visualizations as well as provide modules for downstream analysis of base modifications. Modbamtools comprehensive manual and tutorial can be found at https://rrazaghi.github.io/modbamtools/.