EMS Effect: Mutation Rate Estimation and Sequence Bias Modeling

This repository contains the analysis pipeline for mutation rate estimation and sequence bias modeling of EMS (ethyl methanesulfonate) mutagenesis data, as described in the manuscript.

Documentation

For complete documentation of the analysis pipeline, see manuscript_scope_documentation.md.

Quick Start

The analysis pipeline is contained within the src/rate_modeling/ directory. Key scripts include:

• Data collection: collect_mutation_counts.py, collect_5mer_contexts.py
• Rate estimation: estimate_rates.py
• Sequence bias modeling: sequence_bias_modeling_sitelevel.py
• Visualization: plot_5mer_mutation_rates.py, plot_ems_spectra.py, regenerate_rate_plots.py

Dependencies

See environment.yml for the complete conda environment specification.

Configuration

Reference file paths can be specified in config/reference_paths.yaml or via command-line arguments.