diff --git a/ont/README.md b/ont/README.md index 862ee74..419bc66 100644 --- a/ont/README.md +++ b/ont/README.md @@ -1,9 +1,12 @@ # 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. +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 +## Usage ### `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 ``` -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` @@ -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 ``` -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 @@ -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) - 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 sudo apt-get install git parallel -y