Dmitry Antipov
@dantipov.bsky.social
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Genome assemblers and their friends. Postdoc at
https://genomeinformatics.github.io/
Molecular Mechanisms in Evolution GRC conference short recap
3 months ago
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Verkko2 paper is finally published!
genome.cshlp.org/content/earl...
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Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
https://genome.cshlp.org/content/early/2025/06/11/gr.280383.124.abstract
4 months ago
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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
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He’s anti-democracy and pro-Trump: the obscure ‘dark enlightenment’ blogger influencing the next US administration
Key figures in the incoming administration follow Curtis Yarvin, who’s pushing for an autocratic takeover of the US
https://www.theguardian.com/us-news/2024/dec/21/curtis-yarvin-trump
8 months ago
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Verkko2 paper is finally on the biorxiv
www.biorxiv.org/content/10.1...
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Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
The Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on the semi-manual combination of lo...
https://www.biorxiv.org/content/10.1101/2024.12.20.629807v2
9 months ago
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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
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GitHub - marbl/verkko: Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads. - marbl/verkko
https://github.com/marbl/verkko
about 1 year ago
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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...
over 1 year ago
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Alexey Navalny's death is a disaster for everyone who dreams of free and peaceful Russia
over 1 year ago
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reposted by
Dmitry Antipov
Sergey Nurk
over 1 year ago
One more opening in my group at Oxford Nanopore. This time in our New York office!
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
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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.
over 1 year ago
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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..
almost 2 years ago
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reposted by
Dmitry Antipov
Adam Phillippy
about 2 years ago
"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...
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Ok, let's give this one a try too
about 2 years ago
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you reached the end!!
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