From 39d4380c3dff9cffcb665f20d36ef4ecdd97aa9d Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 30 Mar 2021 09:15:31 -0600
Subject: [PATCH] Create README.md

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+# Oxford Nanopore Technologies
+
+These scripts are for use with a GridION, to make the files and folder structures correspond more closely to those required by downstream bioinformatics programs.
+Note that at the time of writing, the GridION runs Ubuntu 16.04 LTS, and mounts USB drives in the `/data` folder, and these scripts contain some "faults" to work around these idiosyncrasies.
+
+## File Descriptors
+
+### `ont-demux`
+
+```bash
+$ ont-demux FAP_FOLDER
+```
+
+Consolidates all FAST5s into a single gzipped FASTQ using ONT's `guppy_barcoder`. Note that this is for MinKNOW's default settings of 4000 reads/file. It is _highly_ recommended to set the "Number of Reads per File" entry in MinKNOW to 0, and checking "Compress FASTQs" to produce nearly the same results.
+
+### `ont-transfer`
+
+```bash
+$ ont-transfer [-s 1|6|12] FAP_FOLDER
+```
+
+Transfers all of the passing FAST5 and FASTQ files to the first available USB drive, skipping empty barcodes based on the number of the first skip passed through the `-s` parameter, consolidating all files of the same type into one folder for easier sorting and uploading.
+
+## Installation
+
+### Requirements
+
+- git
+- guppy (Get from [ONT Community](https://nanoporetech.com/community)
+- GNU Parallel
+
+See ONT for guppy installation instructions. Others may be installed by opening a terminal and running
+
+```bash
+$ sudo apt-get install git parallel -y
+```
+
+### Instructions
+
+Open a terminal (Ctrl+Alt+T), and use the following commands
+
+```bash
+git clone https://github.com/MillironX/wphl-bioinformatics
+mkdir ~/bin
+echo "export PATH=$PATH:$HOME/bin" >> ~/.bashrc
+cp wphl-bioinformatics/ont/* ~/bin
+chmod +x ~/bin/*
+source ~/.bashrc
+```