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A comprehensive toolkit for running Oxford Nanopore's MinION

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![Poreduck Logo](https://raw.githubusercontent.com/alexiswl/poreduck/master/images/poreduck_logo.png)
# poreduck 
A comprehensive toolkit for running Oxford Nanopore's MinION - symbolised above by this poorly drawn duck.  
*In memory of Jacob & Jacob - two poor ducks.*

poreduck is a set of python built commandline wrappers that can all be run simultaneously to pipe MinION reads
through to analysis in real-time.

poreduck currently can be used for two key steps of handling MinION data:

1.  Transferring of reads from a laptop to a local server or hard-drive in real-time.
2.  Running of a local-basecalling algorithm with

## Tutorials
Checkout this repo:   https://alexiswl.github.io/ASimpleNanoporeTutorial/index.html

## Examples
An examples of poreduck usage is shown below:

### TarMyFast5
```
poreduck tarMyFast5 \
--samplesheet samplesheet.tsv \
--reads_path /var/lib/MinKNOW/data/reads
```

### Basecall the fast5 files.  
```
poreduck albacoreHPC \
--fast5_dir /data/storage/MinION/sample_name/fast5 
--flowcell FLO-MIN106 --kit SQK-LSK108`
where `/data/storage/MinION/sample_name/fast5` contains a list of .tar.gz files each of which holds 4000 fast5 files.
```

## MinKNOW version compatibility
Last tested on MinKNOW version 1.18.02

## Installing Docker - useful for Windows and Mac users.

### Docker Toolbox Installation (Windows based tutorial specific)  
1. Install the docker toolbox from ![docker](https://docs.docker.com/toolbox/)
    + Make sure you download 'docker toolbox', not 'docker for mac' or 'docker for windows'
    + It will ask you if you would like to install Git Bash, say yes, you will need that too.
    + It will ask you if you would like to install Kitematic, say yes, it will be handy.
2. Once docker is installed, open up Kitematic, this will start the docker vm.
3. Open the Git Bash app and confirm that docker has been installed and the VM is loaded by typing `docker --version`

### Docker Toolbox Installation (Mac Users)
Mac users can follow the Windows based tutorial but use the 'Docker Quick Start terminal' instead of 'Git Bash to run the docker commands'

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