Introduction

cmuts is a software suite for processing MaP-seq datasets, as well as its cousins RING-MaP and MOHCA-seq, or more generally any experiment where the readouts are mutations to a known reference sequence.

Web Server

The web server runs cmuts on Hugging Face, bypassing the need for a local install. It is suitable for jobs of a few references and a few thousand reads.

Installing

Each release carries static cmuts binaries for Linux (x86_64, aarch64) and macOS (arm64). These bundle htslib and HDF5, so no libraries need to be installed to run them. Alternatively, you can build from source, which may provide marginal speedups.

cmuts align calls separate programs, which must be on the PATH.

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

brew install minimap2 samtools vsearch
python3 -m pip install h5py numpy plotly

Install Homebrew first if you don’t have it.

apt install minimap2 samtools vsearch
python3 -m pip install h5py numpy plotly

Or load the appropriate modules for your cluster (examples here).

Next Steps