CHMMAIRRa.jl

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.

Quick start

Using the executable

The tool is available as an 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.
CHMMAIRRa --receptor IG --V-fasta V.fasta --assignments MiAIRR.tsv --out CHMMAIRRa_out.tsv

Using the Julia package

using Pkg; Pkg.add("CHMMAIRRa")
using CHMMAIRRa
detect_chimeras_from_files("V.fasta", "MiAIRR.tsv", "CHMMAIRRa_out.tsv", receptor = "IG")

If you are analyzing TCRs, you can use the --receptor TCR argument.

Filter Chimeras from AIRR Dataset

To get your input AIRR file back with chimeras removed (preserving all original columns):

CHMMAIRRa --receptor IG --V-fasta V.fasta --assignments MiAIRR.tsv \
          --out CHMMAIRRa_out.tsv --non-chimeric-MiAIRR filtered_MiAIRR.tsv