Mikhail Kolmogorov

There are no immediate plans for a 3.10 update, but I'll keep this open for the future.

Hi @DaRinker I think the simpler strategy of just using T2T reference for each strain may be sufficient. How much structural variance do you expect between the strains? Otherwise I...

I see, so some genomes are quite distant from each other - then I think it's a good strategy!

Hi Chun - this seems to be an issue with either Cactus or phyloFit, rather than Ragout? If so, it is better to contact the developers of the corresponding tools.

Hi, Wrt to validation, they are usually tailored for particular projects. Your final assembly is based on the information from long reads and the reference genome, so ideally you'd need...

Assuming that this has been answered. Feel free to follow up if you have more questions!

Version 2.9.5 now supports Python 3.12. six is not removed yet, but will be in the next release.

hi @Ge0rges Did you try to compare the flye performance before/after the update on a Q20 data? What's the performance gain? Flye already had specialized minimap2 parameters for `--nano-hq`

Closing due to inactivity - feel free to follow up if you have more questions!

Thanks for reporting! I think this is a problem with the Flye polisher, somehow it generated `polished_1.fasta` file, but not the `base_coverage.bed.gz`. Ultimately the issue is with Flye, but @atabeerk...