novoalab / modPhred

modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

modPhred

modPhred is a pipeline for detection, annotation and visualisation of DNA/RNA modifications from raw ONT data.

The pipeline consists of four steps / modules:

1. modEncode: Encoding modification probabilities in FastQ (mod_encode.py)
2. modAlign: Build alignments keeping modification information in BAMs (mod_align.py)
3. modReport Extraction of RNA modification information (bedGraph) and QC reports (mod_report.py)
4. modAnalysis: Plotting venn diagrams (mod_plot.py), co-occurrence of modifications (mod_correlation.py) and per-read clustering based on modification profiles (mod_cluster.py)

For more information, please visit full documentation at https://modphred.readthedocs.io.

Citation

If you find this work useful, please cite:

Pryszcz LP and Novoa EM (2022) ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. Bioinformatics, 38:257-260.