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# 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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These scripts are for use with a GridION or its output file, to make the files
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and folder 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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contain some "faults" to work around these idiosyncrasies (i.e. they will not
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pass in [ShellCheck]).
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## Usage
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@ -31,7 +32,7 @@ julia --project=PATH_TO_ONT_FOLDER PATH_TO_ONT-RENAME.jl
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In practice, this looks like
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```powershell
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julia --project=C:\Users\MillironX\ont C:\Users\MillironX\illumina\ont-rename.jl
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julia --project=C:\Users\MillironX\ont C:\Users\MillironX\ont\ont-rename.jl
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```
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### `ont-demux` (deprecated)
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@ -45,9 +46,9 @@ same results using far fewer resources and in far less time.**
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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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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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results~~ (this functionality has been taken out of recent updates to MinKNOW).
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## Installation
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@ -56,7 +57,7 @@ results.
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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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- guppy (Get from [ONT 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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@ -71,17 +72,19 @@ sudo apt-get install git parallel -y
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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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git clone https://github.com/MillironX/sc2-sequencing
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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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cp sc2-sequending/ont/* ~/bin
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chmod +x ~/bin/*
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source ~/.bashrc
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```
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### `ont-rename`
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These scripts require [Julia](https://julialang.org).
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These scripts require [Julia].
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Windows install instructions (I will assume Linux users can adapt):
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1. Download and install Julia
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1. Select "Add Julia to PATH" as an option
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@ -97,6 +100,10 @@ These scripts require [Julia](https://julialang.org).
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10. Run `exit()`
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11. Close PowerShell
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12. Right-click the Windows desktop, and click "New | Shortcut..."
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13. Type `julia --project=%USERPROFILE%\ont
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%USERPROFILE%\ont\ont-rename.jl` and click Next
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13. Type `julia --project=%USERPROFILE%\ont %USERPROFILE%\ont\ont-rename.jl` and
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click Next
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14. Type `Rename ONT FASTQs` or something else memorable and click "Finish"
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[ShellCheck]: https://shellcheck.net
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[ONT Community]: https://nanoporetech.com/community
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[Julia]: https://julialang.org
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