Convert org mode README to markdown
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# locigenesis
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locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.
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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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<a id="orgb4db211"></a>
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## Technologies
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- [immuneSIM](https://github.com/GreiffLab/immuneSIM/): in silico generation of human and mouse BCR and TCR repertoires
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- [CuReSim](http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/): read simulator that mimics Ion Torrent sequencing
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<a id="orgace1e30"></a>
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## Installation
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This project uses [Nix](https://nixos.org/) to ensure reproducible builds.
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1. Install Nix (compatible with MacOS, Linux and [WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
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curl -L https://nixos.org/nix/install | sh
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1. Clone the repository:
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git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
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1. Change the working directory to the project:
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cd locigenesis
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1. Enter the nix-shell:
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nix-shell
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After running these commands, you will find yourself in a shell that contains all the needed dependencies.
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<a id="org531bad5"></a>
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## Usage
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An execution script that accepts 2 parameters is provided, the following command invokes it:
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./generation.sh <number of sequences> <number of reads>
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- <number of sequences>: an integer that specifies the number of different sequences to generate
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- <number of reads>: an integer that specifies the number of reads to perform on each sequence
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The script will generate 2 files under the data directory:
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<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
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<col class="org-left" />
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<col class="org-left" />
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</colgroup>
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<tbody>
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<tr>
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<td class="org-left">HVR.fastq</td>
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<td class="org-left">Contains the original CDR3 sequence</td>
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</tr>
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<tr>
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<td class="org-left">CuReSim-HVR.fastq</td>
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<td class="org-left">Contains CDR3 after the read simulation, with sequencing errors</td>
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</tr>
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</tbody>
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</table>
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56
README.org
56
README.org
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@ -1,56 +0,0 @@
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* locigenesis
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locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.
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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
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- [[https://github.com/GreiffLab/immuneSIM/][immuneSIM]]: in silico generation of human and mouse BCR and TCR repertoires
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- [[http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/][CuReSim]]: read simulator that mimics Ion Torrent sequencing
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** Installation
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This project uses [[https://nixos.org/][Nix]] to ensure reproducible builds.
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1. Install Nix (compatible with MacOS, Linux and [[https://docs.microsoft.com/en-us/windows/wsl/about][WSL]]):
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#+begin_src shell
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curl -L https://nixos.org/nix/install | sh
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#+end_src
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1. Clone the repository:
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#+begin_src shell
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git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
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#+end_src
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3. Change the working directory to the project:
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#+begin_src shell
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cd locigenesis
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#+end_src
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4. Enter the nix-shell:
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#+begin_src shell
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nix-shell
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#+end_src
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After running these commands, you will find yourself in a shell that contains all the needed dependencies.
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** Usage
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An execution script that accepts 2 parameters is provided, the following command invokes it:
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#+begin_src shell
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./generation.sh <number of sequences> <number of reads>
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#+end_src
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- <number of sequences>: an integer that specifies the number of different sequences to generate
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- <number of reads>: an integer that specifies the number of reads to perform on each sequence
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The script will generate 2 files under the data directory:
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| HVR.fastq | Contains the original CDR3 sequence |
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| CuReSim-HVR.fastq | Contains CDR3 after the read simulation, with sequencing errors |
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