Parameters for R9 Guppy2, 4, 6 about dysgu HOT 4 CLOSED

Hi @StellariaYuki,
Currently the default parameters are set to work well with low error rate ONT reads such as those generated using the newer Kit14 work flow HAC or SUP models. The divergence of older kits should be set higher on account of the higher error rate. Using auto will generally set a conservative value. Dropping the divergence can improve sensitivity around multiallelic sites, although the number of duplicate true positives will increase.
Did you try the auto setting?

from dysgu.

Thank you very much for your prompt response @kcleal. Based on my understanding, I believe the appropriate setting for R9Guppy2,4,6 data, including Guppy6 data in HAC mode, should be "--max-cov auto --divergence auto". Could you kindly confirm if my understanding is correct?

from dysgu.

Yes, they should work well. But pay attention to the output messages printed to the terminal by dysgu, they will tell you what the inferred values were, and you can compare to the default values

from dysgu.

@kcleal Thanks a lot, have a nice day!

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