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haotianteng / Chiron

A basecaller for Oxford Nanopore Technologies' sequencers
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chunks consensus #120

Closed F0nz0 closed 9 months ago

F0nz0 commented 1 year ago

Hi and thank you very much for your very interesting paper and tool. I would really appretiate to receive some additional information about Chiron. More in detail, I'm facing with a similar task and I'm trying to find inside your code how you merged overlapping chunks to produce the final basecalled reads, but I haven't been able to do that. Could you indicate the script performing this task (finding consensus sequence between contiguous chunks of outputs produced during the basecalling step) ?

Thank you very much in advance Best Regards.

haotianteng commented 9 months ago

It's in this scripit: chiron/utils/easy_assembler.py

There are several different assembly methods depending on the jump ratio, the default one is a simple sticking method, i.e. simply concatenate the chunks.