Pipeline

The cmuts pipeline consists of three main programs:

1. cmuts align - Alignment and preprocessing wrapper (uses bowtie2, samtools, fastp)
2. cmuts core - Mutation counting engine (use --pairwise flag for 2D MaP-seq data)
3. cmuts normalize - Normalization and reactivity profile generation (handles both 1D and 2D data automatically)

Warning

Some sequencing vendors (e.g. Ultima) will provide pre-aligned BAM/CRAM files. In such a case, simply ignore the cmuts align step.

Optional Tools

• cmuts plot - Plot reactivity profiles from HDF5 files
• cmuts visualize - Overlay reactivities on 3D structures (requires ChimeraX)
• cmuts generate - Generate synthetic test data for validation
• cmuts test - Run the integration test suite