Genome assemblers and their friends. Postdoc at https://genomeinformatics.github.io/ https://bsky.app/profile/dantipov.bsky.socialhttps://bsky.app/profile/dantipov.bsky.social/post/3mhbvbpsxbk2vgithub 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?17 Mar 2026 21:13 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3mhbvbpsxbk2vhttps://bsky.app/profile/dantipov.bsky.social/post/3mgvbixyfec2tThis is the first time I've actually used an Eulerian path algorithm in genome assembly. https://www.biorxiv.org/content/10.64898/2026.03.06.710180v1 github.com/marbl/TTT12 Mar 2026 20:47 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3mgvbixyfec2thttps://bsky.app/profile/dantipov.bsky.social/post/3lsmecqrnjk2nMolecular Mechanisms in Evolution GRC conference short recap27 Jun 2025 19:20 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3lsmecqrnjk2nhttps://bsky.app/profile/dantipov.bsky.social/post/3lrgziqn25k2rVerkko2 paper is finally published! https://genome.cshlp.org/content/early/2025/06/11/gr.280383.124.abstract12 Jun 2025 22:58 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3lrgziqn25k2rhttps://bsky.app/profile/dantipov.bsky.social/post/3lhfewltdlc2zI believe this to be one of the most important things now. https://www.theguardian.com/us-news/2024/dec/21/curtis-yarvin-trump 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 news05 Feb 2025 01:05 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3lhfewltdlc2zhttps://bsky.app/profile/dantipov.bsky.social/post/3lecrgl6zsk2gVerkko2 paper is finally on the biorxiv https://www.biorxiv.org/content/10.1101/2024.12.20.629807v227 Dec 2024 19:55 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3lecrgl6zsk2ghttps://bsky.app/profile/dantipov.bsky.social/post/3l327xaxwva2iFinally 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 https://github.com/marbl/verkko31 Aug 2024 21:34 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3l327xaxwva2ihttps://bsky.app/profile/dantipov.bsky.social/post/3knmibdot242zWant 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 https://www.nature.com/articles/s41592-023-02141-113 Mar 2024 23:58 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3knmibdot242zhttps://bsky.app/profile/dantipov.bsky.social/post/3klkwmxx54s2bAlexey Navalny's death is a disaster for everyone who dreams of free and peaceful Russia16 Feb 2024 22:20 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3klkwmxx54s2bhttps://bsky.app/profile/dantipov.bsky.social/post/3kkwdqw3o3r2uFinally 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.08 Feb 2024 17:49 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3kkwdqw3o3r2uhttps://bsky.app/profile/dantipov.bsky.social/post/3kcqzdk4okp2dConsider 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..27 Oct 2023 19:37 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3kcqzdk4okp2dhttps://bsky.app/profile/dantipov.bsky.social/post/3k6tujpmq622jOk, let's give this one a try too08 Sep 2023 01:09 +0000at://did:plc:3ixihniligiwyiuhmplgp3g2/app.bsky.feed.post/3k6tujpmq622j