Pryszcz, Leszek Piotr, 1985-Novoa, Eva Maria2021-11-292021-11-292022Pryszcz LP, Novoa EM. ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. Bioinformatics. 2022;38(1):257-60. DOI: 10.1093/bioinformatics/btab5391367-4803http://hdl.handle.net/10230/49079Motivation: DNA 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. Results: Here 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: ModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license. Docker images with all dependencies preinstalled are also provided. Supplementary information: Supplementary data are available at Bioinformatics online.application/pdfeng© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/bioinformatics/btab539info:eu-repo/semantics/openAccess