github copilot CLI: you need a special approval from your organization to use it with copilot-provided models opencode CLI(alternative 3rd-party tool, supported by github): you are welcome to use copilot-provided models, no approval needed. Logic?

This is the first time I've actually used an Eulerian path algorithm in genome assembly. www.biorxiv.org/content/10.6... github.com/marbl/TTT

Molecular Mechanisms in Evolution GRC conference short recap

Verkko2 paper is finally published! genome.cshlp.org/content/earl...

I believe this to be one of the most important things now. www.theguardian.com/us-news/2024... Guardian missed that this guy is also a long-time business partner of Peter Thiel and is really influential among those tech bros. I've read his manifestos. They are frightening and really match the news

Verkko2 paper is finally on the biorxiv www.biorxiv.org/content/10.1...

Finally on some samples we have all 46 human chromosomes T2T. Update to verkko 2.2, last big release of this summer! github.com/marbl/verkko

Want to discuss a thing about reviewing process. It is far from "ai-generated alpha male rat" level of weirdness, but still weird for me, and I really do not know how it should be fixed. Let's look on the article on diploid aware polisher. Published just a week ago www.nature.com/articles/s41...

Alexey Navalny's death is a disaster for everyone who dreams of free and peaceful Russia

One more opening in my group at Oxford Nanopore. This time in our New York office! ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...

Finally verkko 2.0 is out! github.com/marbl/verkko Waiting for your bug reports;) My dream for 46 t2t scaffolds on the de novo human genome assemblies out of the box is still a dream, but for some samples we are really close.

Consider a DAG with edges having both weight and length. Problem: find a path between given vertices with highest _average_ weight (= total_w/total_l). Is it known to be NP-hard in general case? Looks similar to 0-1 knapsack, but I failed to construct polynomial reduction..

"Minmers are a generalization of minimizers that enable unbiased local jaccard estimation" aka MashMap3 with Bryce Kille, @erikg.bsky.social, and @treangen.bsky.social is now accepted in Bioinformatics! Many thanks to the reviewers for their very careful reviews doi.org/10.1093/bioi...

Ok, let's give this one a try too