CHMMAIRRa.jl is a method for reference-based detection of chimeric adaptive immune receptor repertoire (AIRR) sequences.
We use a Hidden Markov Model (HMM) to represent sequences as being generated from a single reference with mutations or from multiple references with mutations. The core HMM functionality is implemented in the CHMMera.jl package, while CHMMAIRRa.jl provides an AIRR-specific wrapper for the HMM.
The tool is primarily distributed as a an executable for Linux and MacOS from the releases page. Once you have downloaded the executable, you will need to unpack it and add it to your PATH to allow it to be run from any directory in the terminal.
unzip CHMMAIRRa_ubuntu-linux_x86-64_v0.0.1.zip # unpack the executable
export PATH=$PATH:$(pwd)/CHMMAIRRa_ubuntu-linux_x86-64_v0.0.1/bin/ # add the executable to your PATH. Place this line in your ~/.bashrc or ~/.zshrc file to make it permanent.
The tool is also available from the Julia package manager.
For chimera detection with a minimal output, run the following command:
CHMMAIRRa --receptor IG --V-fasta V.fasta --assignments AIRR.tsv --out CHMMAIRRa_out.tsv