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49 lines
1.6 KiB
Markdown
49 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 structures correspond more closely to those required by downstream bioinformatics programs.
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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.
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## File Descriptors
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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 `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.
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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 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.
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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 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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