A simple application for merging and renaming Oxford Nanopore barcode FASTQ.GZ files on the machine it was sequenced.
The app detects barcode folders inside a default structured ONT fastq_pass folder, lets the user enter sample names in the browser, and creates one merged .fastq.gz file per sample.
An ONT run folder containing:
fastq_pass/
fastq_fail/
pod5/
git clone https://github.com/microbemarsh/ont_fastq_app.git
cd ont_fastq_app
./ont_fastq_app
ONT sequencing is used by a lot of labs without a great understanding of CLI commands. This app can enable users to take their basecalled fastq.gz file directly from their sequencing PC and upload to shared folders or to servers for collaborators to process the rest of the data.
One use case I'd like to highlight is that non-CLI people could sequence their sample/s, run ont_fastq_app and then upload their fastq.gz and samplesheet.csv into tools like Omi for further help processing their own data!