mirror of
https://github.com/MillironX/sc2-sequencing.git
synced 2024-12-22 11:18:17 +00:00
50 lines
1.6 KiB
Markdown
50 lines
1.6 KiB
Markdown
|
# 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.
|
||
|
|
|
||
|
|
## File Descriptors
|
||
|
|
|
||
|
|
### `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
|
||
|
|
```
|