# 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.


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## 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


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## 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)):

    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.


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## 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:

<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">


<colgroup>
<col  class="org-left" />

<col  class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left">HVR.fastq</td>
<td class="org-left">Contains the original CDR3 sequence</td>
</tr>


<tr>
<td class="org-left">CuReSim-HVR.fastq</td>
<td class="org-left">Contains CDR3 after the read simulation, with sequencing errors</td>
</tr>
</tbody>
</table>