ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data

MotivationDNA and RNA modifications can now be identified using Nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. ResultsHere we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner. Availability and ImplementationModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license. Supplementary DataSupplementary Data are available at Bioinformatics online.