# 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](https://github.com/GreiffLab/immuneSIM/): in silico
    generation of human and mouse BCR and TCR repertoires
-   [CuReSim](http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/):
    read simulator that mimics Ion Torrent sequencing

## Installation

This project uses [Nix](https://nixos.org/) to ensure reproducible
builds.

1.  Install Nix (compatible with MacOS, Linux and
    [WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):

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

2.  Clone the repository:

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

3.  Change the working directory to the project:

```bash
cd locigenesis
```

4.  Enter the nix-shell:

```bash
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:

```bash
./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
  ------------------- -----------------------------------------------------------------