cmuts

Fast, multithreaded pair-HMM counting of MaP-seq mutations.

Installing

Each release carries static cmuts binaries for Linux (x86_64, aarch64) and macOS (arm64). These are self-contained and have no dependencies. Alternatively, you can build from source, which may provide marginal speedups.

The bundled cmuts-align helper requires

• minimap2
• samtools
• fastp for paired-end input.

On macOS with Homebrew:

brew install minimap2 samtools fastp

On Debian and Ubuntu:

apt install minimap2 samtools fastp

The bundled cmuts-plot helper requires a Python 3 installation with the h5py, numpy, and plotly packages.

python3 -m pip install h5py numpy plotly

Usage

Compute reactivity rates via the pair HMM on a specific experiment:

cmuts hmm -f references.fasta -o treated.h5 treated.bam

Subtract rates computed from multiple experiments:

cmuts sub -o reactivity.h5 treated.h5 untreated.h5

Normalize reactivity rates across experiments:

cmuts norm -o apo-normalized.h5 -o holo-normalized.h5 apo.h5 holo.h5

Generate an interactive report of the results:

cmuts plot \
    apo-normalized.h5 --label "Apo" \
    holo-normalized.h5 --label "Holo"

Documentation

See the docs for more details on each program, the HDF5 outputs, and special use cases.

Development

See CONTRIBUTING.md for information on development builds and running tests.