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Cleanup ONT README

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Thomas A. Christensen II 2021-04-13 13:56:10 -06:00
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ont/README.md
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# Oxford Nanopore Technologies # 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. These scripts are for use with a GridION, to make the files and folder
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. 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 ## Usage
### `ont-demux` ### `ont-demux`
@ -11,7 +14,11 @@ Note that at the time of writing, the GridION runs Ubuntu 16.04 LTS, and mounts
ont-demux FAP_FOLDER 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. 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` ### `ont-transfer`
@ -19,7 +26,10 @@ Consolidates all FAST5s into a single gzipped FASTQ using ONT's `guppy_barcoder`
ont-transfer [-s 1|6|12] FAP_FOLDER 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. 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 ## Installation
@ -29,7 +39,8 @@ Transfers all of the passing FAST5 and FASTQ files to the first available USB dr
- guppy (Get from [ONT Community](https://nanoporetech.com/community) - guppy (Get from [ONT Community](https://nanoporetech.com/community)
- GNU Parallel - GNU Parallel
See ONT for guppy installation instructions. Others may be installed by opening a terminal and running See ONT for guppy installation instructions. Others may be installed by opening
a terminal and running
```bash ```bash
sudo apt-get install git parallel -y sudo apt-get install git parallel -y