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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Duplex basecalling without cutting/trimming adaptors #679

Closed pclavell closed 5 months ago

pclavell commented 6 months ago

I'd like to perform a duplex basecalling without trimming the adaptors as I later want to use a linker contained after the 5' adaptor to demultiplex. However, the parameter --no-trim is not available for dorado duplex function. Is there any workaround for this?

tijyojwad commented 5 months ago

Hi @pclavell - the way our duplex pairing heuristics work will result in the adapter getting trimmed off.

However, each duplex read tracks the parent reads they came from (the read id is parent_read1;parent_read2). So you can demultiplex the parent simplex read (which won't be trimmed in the duplex pipeline) and use that information to then demux the duplex offspring.

pclavell commented 5 months ago

Hi @tijyojwad , so I understand that in dorado duplex, by default, all simplex reads (independently of having a pair read, and therefore an associate duplex) are not trimmed and they preserve ONT adapters and any other adjacent primer.

tijyojwad commented 5 months ago

yes that's correct