Maria Nattestad

Looking at your [other issue](https://github.com/PacificBiosciences/harmony/issues/1), I think you might get better results on DeepConsensus by just following the DeepConsensus quick start more closely, like using `ccs --all` and just making...

Thanks for the heads up. I don't have access to that server anymore, so I asked Mike who still does. We'll get back to you when it's (hopefully easily) fixed.

Yes. One of the examples is E. coli. I’d experiment with lower parameters when the genome is tiny, for alignment and for Assemblytics, just a matter of trying things to...

Ah yes I've seen issues with R packages for my tutorial videos where code that used to work is not compatible with future versions. I think in Python it's better,...

I think so, but it’s been a long time, so I’m not sure. I recommend checking it, e.g. by looking at one of the smaller examples, which should also help...

Hi Giovanni Have you tried other scripts for converting sam to delta? Assemblytics calls variants largely by simply parsing the delta file, which I verified extensively with MUMmer show-aligns to...

Looks like the whole institute’s server is down. I’ll check in on it.

You have long-range SVs in the malaria genome? Interesting! It should be pretty easy to register a new reference genome annotation by forking this repo and then: 1. Adding your...

I'm not that surprised, just interested. I've mostly worked with human genomes, and humans have a lot less variation between individuals, so having enough long-range SVs to make SplitThreader useful...

Okay, so it might be too much for you to try to debug this if you don't really have much coding experience, and I can't really help you with it...