Convert org mode README to markdown

README.md

@@ -1,75 +1,69 @@
 # locigenesis
 
-locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.
+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>
+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
-
-
-<a id="orgace1e30"></a>
+-   [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.
+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)):
+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
+``` {.shell}
+curl -L https://nixos.org/nix/install | sh
+```
 
 1.  Clone the repository:
 
-    git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
+``` {.shell}
+git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
+```
 
 1.  Change the working directory to the project:
 
-    cd locigenesis
+``` {.shell}
+cd locigenesis
+```
 
 1.  Enter the nix-shell:
 
-    nix-shell
+``` {.shell}
+nix-shell
+```
 
-After running these commands, you will find yourself in a shell that contains all the needed dependencies.
-
-
-<a id="org531bad5"></a>
+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:
+An execution script that accepts 2 parameters is provided, the following
+command invokes it:
 
-    ./generation.sh <number of sequences> <number of reads>
+``` {.shell}
+./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
+-   \<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>
-
+  ------------------- -----------------------------------------------------------------
+  HVR.fastq           Contains the original CDR3 sequence
+  CuReSim-HVR.fastq   Contains CDR3 after the read simulation, with sequencing errors
+  ------------------- -----------------------------------------------------------------