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