Base modification analysis in long read sequencing data using Minimod

Recent advances in long read sequencing technologies have enabled the detection of various DNA and RNA base modifications in addition to standard nucleotide sequences. Both major vendors in this space—Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio)—now include base modification information in their sequencing outputs using MM/ML tags embedded in unaligned BAM files. Each vendor also provides dedicated tools for extracting and analysing these tags, such as ONT’s modkit and PacBio’s pb-CpG-tools. This work presents minimod, a new vendor-agnostic tool designed to extract and analyse any type of base modification from sequencing data generated by any platform that supports MM/ML tags. Benchmarking demonstrates that for DNA data, minimod is ~1.25× faster on a server and ~4× on a laptop compared to modkit and pb-CpG-tools. For RNA data, minimod achieves even greater speedups compared to modkit, ~12× on the server and ~55× on the laptop. Minimod is a free, open-source application written in C and is available at https://github.com/warp9seq/minimod .