From 6561aa2caf1e998f60abed4064f040a726ae3a48 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Wed, 5 May 2021 12:19:40 +0200
Subject: [PATCH] Convert org mode README to markdown

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 README.org | 56 ----------------------------------------
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 delete mode 100644 README.org

diff --git a/README.md b/README.md
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+# 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.
+
+
+<a id="orgb4db211"></a>
+
+## 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
+
+
+<a id="orgace1e30"></a>
+
+## 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.
+
+
+<a id="org531bad5"></a>
+
+## 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>
+
diff --git a/README.org b/README.org
deleted file mode 100644
index f51bc55..0000000
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-* 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
-
-- [[https://github.com/GreiffLab/immuneSIM/][immuneSIM]]: in silico generation of human and mouse BCR and TCR repertoires
-- [[http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/][CuReSim]]: read simulator that mimics Ion Torrent sequencing
-
-** Installation
-
-This project uses [[https://nixos.org/][Nix]] to ensure reproducible builds.
-
-1. Install Nix (compatible with MacOS, Linux and [[https://docs.microsoft.com/en-us/windows/wsl/about][WSL]]):
-
-#+begin_src shell
-curl -L https://nixos.org/nix/install | sh
-#+end_src
-
-1. Clone the repository:
-
-#+begin_src shell
-git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
-#+end_src
-
-3. Change the working directory to the project:
-
-#+begin_src shell
-cd locigenesis
-#+end_src
-
-4. Enter the nix-shell:
-
-#+begin_src shell
-nix-shell
-#+end_src
-
-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:
-
-#+begin_src shell
-./generation.sh <number of sequences> <number of reads>
-#+end_src
-
-- <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 |