https://github.com/murrellgroup/chmmairra.jl

https://github.com/murrellgroup/chmmairra.jl

Last synced: 5 months ago
JSON representation

• Host: GitHub
• URL: https://github.com/murrellgroup/chmmairra.jl
• Owner: MurrellGroup
• License: mit
• Created: 2024-11-14T16:58:47.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-02-24T15:31:08.000Z (over 1 year ago)
• Last Synced: 2025-02-28T20:22:32.586Z (over 1 year ago)
• Language: Julia
• Homepage:
• Size: 257 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          
# CHMMAIRRa.jl

[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://murrellgroup.github.io/CHMMAIRRa.jl/)

[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/license/MIT)

[![Coverage](https://codecov.io/gh/MurrellGroup/CHMMAIRRa.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/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](https://github.com/MurrellGroup/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](https://github.com/MurrellGroup/CHMMAIRRa.jl/releases). You will need to unpack it and add it to your PATH to allow it to be run from any directory in the terminal.

```bash

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

```julia

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):

```bash

CHMMAIRRa --receptor IG --V-fasta V.fasta --assignments MiAIRR.tsv \

          --out CHMMAIRRa_out.tsv --non-chimeric-MiAIRR filtered_MiAIRR.tsv

```