Chris Wright

@rob234king Please try v1.7.0, which contains some amendments to the `smolecule` command to fix this issue in at least some circumstnaces.

I agree there's some unfortunate confusion here. The is indeed a close connection between the guppy model used and the appropriate medaka model. Guppy however has a variety of methods...

Hi @Kirk3gaard, This is something that's been on the to do list for a long time but gets pushed down the priorities with medaka being focussed on research. We'd implement...

Hi @pbelmann, From where has your data come? It might be the case that the fastq headers contain useful information that can help us advise you. Failing that, if you...

The basecaller version and model is encoded in the fastq headers for more recent data, older datasets will not have this. The guppy CHANGELOG contains release dates. I don't know...

The MinION is the best model I can suggest. I will raise an internal issue to train a model for Flongle.

The warning cam be safely ignored. I'm not sure why the code emits it because if I recall correctly there is a guard against it happening. We'll take a look.

We have not performed a systematic study of the effect of varying the minimap2 parameters recently. However the consensus model in medaka is trained against alignments using the parameters as...

Hi @alantsangmb, I don't think it likely that this feature be implemented. At its heard medaka is a consensus caller, not a variant caller -- it is not setup to...

@jpn2021 @kirk3gaard It looks like an oversight that `medaka_haploid_variant` doesn't take a `--regions` argument like other programs. We can look at adding that. More generally the medaka programs don't implement...