ONT Basecalling Update to Dorado and Pod5- What does this mean for DeepRepeat?

[natashaberthold]

Hi all,
I am new to both ONT and variant calling, and have come across DeepRepeat in a number of articles around genotyping microsats. The usage instrcutions in the ReadMe file state that you are required to inpuit fast5 files with a fast5 index and these must be basecalled with Albacore. In light of the fact that Albacore is now quite out of date, and the latest basecaller, dorado, outputs Pod5 files what does this mean for DeepRepeat? Will it be updated to be compatible with Pod5?
Cheers!

[kaichop]

If you are interested to quantify known repeats, you can use the latest basecaller with high accuracy mode and then use NanoRepeat to infer repeats. If you want to predict novel expansions, then this has to be called by Albacore due to the need to use an event table in the current model.

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On Tue, Sep 5, 2023 at 5:04 AM Natasha Berthold ***@***.***> wrote: Hi all, I am new to both ONT and variant calling, and have come across DeepRepeat in a number of articles around genotyping microsats. The usage instrcutions in the ReadMe file state that you are required to inpuit fast5 files with a fast5 index and these must be basecalled with Albacore. In light of the fact that Albacore is now quite out of date, and the latest basecaller, dorado, outputs Pod5 files what does this mean for DeepRepeat? Will it be updated to be compatible with Pod5? Cheers! — Reply to this email directly, view it on GitHub <#15>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OFIFEUMYBOA6EX4IO3XY3TJZANCNFSM6AAAAAA4LOFLCE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>