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JWDebler / nanopore_kit14_assembly

fungal genome assembly from Q20+ nanopore reads
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basecalling.sh - SUP needed for initial calling? #1

Open DntBScrdDv opened 3 months ago

DntBScrdDv commented 3 months ago

Hi,

First - thank you so much for this script, and the workaround for demuxing duplex reads. It's exactly what I needed.

I just have a question regarding the initial basecalling - is there a reason this should be SUP? If I understood correctly, this first basecalling step is to allow the initial demuxing, from where the duplex basecalling can be done.

To save (considerable) computing time, could this not be HAC?

Thanks again!

JWDebler commented 3 months ago

Hi mate, you are correct, SUP at this stage might be overkill. The only reads that will be used from the initial SUP call are the split reads that stem from concatenation of reads from different barcodes, everything else gets extracted from the duplex called ones. Since the split reads only make up a tiny fraction HAC calling should be more than enough for the demultiplexing. Good catch. Cheers.