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Splitting concatemers with internal adapters without basecalling #1192

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britnyblu opened this issue Dec 22, 2024 · 1 comment
Open

Splitting concatemers with internal adapters without basecalling #1192

britnyblu opened this issue Dec 22, 2024 · 1 comment

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@britnyblu
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From what I understand, basecalling via dorado now includes splitting concatemers.

  1. Is there an option (or plans for an option) to split on internal adapters and not just the ONT adapters?
  2. Is there a way to perform this step after basecalling? I have fastqs which have already been basecalled and in addition to multiplexing I would like to split potential concatemers.
    Thanks
@malton-ont
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Hi @britnyblu,

Dorado only splits on ONT adapters at present. You may want to investigate porechop - note that this is a 3rd party tool and looks to have been out of development for some time, so your mileage may vary.

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@britnyblu @malton-ont