minimod

minimod extracts and analyses base modifications from sequencing data that uses MM/ML tags in unaligned BAM files.

Key Features:

• Vendor independence: minimod processes base modification data from both Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) platforms without requiring vendor-specific tools.
• Performance: For DNA data, minimod operates ~1.3-1.6× faster on a server and ~4× faster on a laptop compared to modkit and pb-CpG-tools; for RNA data, it achieves ~12× faster performance on a server and ~55× on a laptop compared to modkit.
• Base modification frequency calculation: minimod calculates base modification frequencies from BAM files containing MM/ML tags.
• Base modification viewing: minimod provides functionality to view base modifications stored in BAM files.

Scientific Applications:

• DNA base modification analysis: minimod enables extraction and analysis of DNA base modifications from long-read sequencing data with MM/ML tags.
• RNA base modification analysis: minimod supports extraction and analysis of RNA base modifications from long-read sequencing data with MM/ML tags.
• Cross-platform epigenetic studies: minimod facilitates comparative analysis of base modifications across different sequencing platforms by using a unified tool for both ONT and PacBio data.

Methodology:

minimod is written in C and processes MM/ML tags embedded in unaligned BAM files to extract and analyse base modifications.