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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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All Context 5mC and 6mA model for R9.4.1 #228

Closed partha434 closed 2 months ago

partha434 commented 1 year ago

Please release dorado all context 5mC and 6mA model for r9.4.1 flow cell...🙏🏻🙏🏻🙏🏻

engelbrechte commented 1 year ago

Seconded, would really appreciate this. 6mA 9.4.1 would help for analysis of early DiMeLo-seq data.

bely12 commented 5 months ago

How can 6mA modifications be called if the 9.4.1 flow cell was used? Do I need to look outside ONT packages to achieve this? Any suggestions would be appreciated, I'm new to nanopore data analysis.

marcus1487 commented 5 months ago

We do not plan to release an R9 all-context 5mC or 6mA model outside of the research model released in the Rerio repository. This model is only applicable in Guppy and is based off of the deprecated flip-flop modified base structure which effects the basecalls while making modified base calls.

The R9 chemistry models never achieved high enough all-context modified base accuracy for a production release and thus the strong recommendation is to upgrade to the R10 chemistry and apply the current models. It is a significant effort to train the all-context modified base models to sufficient accuracy and involves utilizing the duplex chemistry which is not available for R9 flowcells. For all of these reasons we have not plans to train and release any R9 chemistry all-context models.