1.4 KiB
1.4 KiB
locigenesis
locigenesis is a tool that generates an immune repertoire and runs it through a sequence reader simulation tool, to generate sequencing errors.
Installation
This project uses Nix to ensure reproducible builds.
- Install Nix (compatible with MacOS, Linux and WSL):
curl -L https://nixos.org/nix/install | sh- Clone the repository:
git clone https://git.coolneng.duckdns.org/coolneng/locigenesis- Change the working directory to the project:
cd locigenesis- Enter the nix-shell:
nix-shellAfter 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 |