sc2-sequencing/ont/README.md

# 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.

## Usage

### `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
```