Building a pseudo-hybrid reference genome

1:17:40CC19 and CC37. >> Now when you sequence the offspring's DNA, right? Usually when you want to put together even when you've got these long reads, you've got to have a reference genome to put stuff together to. But we don't really have a reference genome for the offspring of these two lines, right? And it's not great to just use one or the other because you really you're going to have to have like some middle ground. And so one thing that I do want to talk about is like in traditional bioinformatics pipelines, right? You've got these and I think um photo 30 will show that in a traditional bioinformatics pipeline, right? you've got fragmented DNA, even if they're long, you sequence the DNA, then you get

1:18:21all these unaligned sequences and then you try to align those sequences to a reference genome. Okay? And the reference genome is something that you get like if you've got a human genetics, right? You've got the human genome project and you align your own DNA to that because there's not going to be that many differences, right? But here, those tiny differences are going to matter in this study, right? And so what they did was they actually solved it by constructing a pseudohybrid intermediate genome which is I think very cool that they were careful enough you know to create this kind of custom software that constructs um a synthetic reference genome for every single cross right and um it includes all of the strain specific insertions of the parent

1:19:02genomes but it's like unbiased analysis of what the >> um what the kids are going to be showing. Mhm. Mhm. >> In terms of methylation. >> And that this this is important because again that reference genome is otherwise you're kind of you have no you have literally no reference. >> Yeah. Exactly. And then it's impossible but you can't use one or the other. You got to use this like hybrid. And so they were careful enough to do that. I thought that was quite cool. >> That's a that's an important and again shows the the they're really trying to do it in a robust >> Yeah. very meticulously >> uh fashion especially also from a replication perspective. >> Exactly. Yeah. So now we can finally get to the results figures. Okay. Yes. >> So, um let's talk about the control.