ModPhred

ModPhred encodes, preserves, extracts, and analyzes DNA and RNA modification probabilities within sequencing data to enable per-read modification profiling and visualization.

Key Features:

• Encoding Modification Probabilities: modEncode encodes DNA and RNA modification probabilities directly into FastQ files.
• Alignment with Modification Information: modAlign constructs alignments while preserving modification data within BAM files.
• Data Extraction and Quality Control: modReport extracts RNA modification information and generates quality-control reports.
• Advanced Visualization and Analysis: modAnalysis provides visualization and analysis including Venn diagrams via mod_plot.py, co-occurrence analysis of modifications, and per-read clustering based on modification profiles.

Scientific Applications:

• Epigenetics and transcriptomics: Enables analysis of DNA and RNA modifications relevant to epigenetic and transcriptomic studies.
• Read-level visualization: Facilitates integration of modification data into genomic track viewers for granular, per-read visualization.
• Biological mechanism studies: Supports investigations into gene regulation, disease mechanisms, and evolutionary biology via modification profiling.

Methodology:

modEncode writes modification probabilities into FastQ; modAlign preserves modification data in BAM during alignment; modReport extracts RNA modification information and produces QC reports; modAnalysis generates plots (including Venn diagrams via mod_plot.py), assesses modification co-occurrence, and performs per-read clustering; the software is implemented in Python3.