locigenesis/README.org

• locigenesis
  • Technologies
  • Installation
  • Usage

locigenesis

locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.

The goal of this project is to generate both HVR sequences with and without sequencing errors, in order to create datasets for a Machine Learning algorithm.

Technologies

• immuneSIM: in silico generation of human and mouse BCR and TCR repertoires
• CuReSim: read simulator that mimics Ion Torrent sequencing

Installation

This project uses Nix to ensure reproducible builds.

1. Install Nix (compatible with MacOS, Linux and WSL):

curl -L https://nixos.org/nix/install | sh

1. Clone the repository:

git clone https://git.coolneng.duckdns.org/coolneng/locigenesis

1. Change the working directory to the project:

cd locigenesis

1. Enter the nix-shell:

nix-shell

After running these commands, you will find yourself in a shell that contains all the needed dependencies.

Usage

An execution script that accepts 2 parameters is provided, the following command invokes it:

./generation.sh <number of sequences> <number of reads>

• <number of sequences>: an integer that specifies the number of different sequences to generate
• <number of reads>: an integer that specifies the number of reads to perform on each sequence

The script will generate 2 files under the data directory:

HVR.fastq	Contains the original CDR3 sequence
CuReSim-HVR.fastq	Contains CDR3 after the read simulation, with sequencing errors