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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Expected release of all-context methylation models for kit 12? #252

Open Kirk3gaard opened 2 years ago

Kirk3gaard commented 2 years ago

Hi

Any estimate on when we can expect to get methylation models for kit 12? I have experienced a growing interest in getting bacterial genomes with methylation profiling after kit 12 showed that nanopore only assemblies was achievable.

Best regards Rasmus

marcus1487 commented 2 years ago

We do not have an expected date of release for all-context methylation models at this time. We do have good evidence internally that R10.4 kit 12 (aka E8.1 motor) does provide increased performance on 6mA (as well as the presented 5mC in CpG context), but are still in the research phase on all-context models. These initial 6mA results were achieved using known zymo bacterial motifs for 6mA as training data, but we are working on other avenues to produce models which will contain virtually all contexts. Once we have these models trained and validated they will be released to the community.

Kirk3gaard commented 2 years ago

Hi Marcus

That sounds great. Really looking forward to it.

Best regards Rasmus