I recently got fastQ files from a MinION sequencer. I would like to demultiplex these files.
Is there any other software to demultiplex (no porechop) in or outside Artic protocol? I would like to learn options different from porechop.
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The Guppy basecaller itself now has the ability to internally perform multiplexing. That is currently the preferred option.
If for some reason, you still want a stand-alone application to demultiplex already basecalled reads, then
qcat is an option: https://github.com/nanoporetech/qcat
I have written up my own semi-manual method for demultiplexing Nanopore reads. As distinct from the other methods that are commonly used, it searches the entire read for potential barcode sequences, and splits out identified chimeric reads (containing multiple barcode sequences) into a separate file: