Sergey Koren

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references - Genome Biology Background Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ult...

Our hitchhiking paper is out at genomebiology.biomedcentral.com/articles/10.... great collaborative effort with Prasad Sarashetti, @jlipovac.bsky.social, Filip Tomas and JJ Liu.
Briefly, the nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3

Thanks @rrwick.bsky.social. Bri is enjoying a well-deserved retirement after working on assembly for over 25 years. I suspect we may have some patch releases but no major changes/features.

Long-read special issue of GR is out, including our paper on T2T assembly using only Nanopore. Just in time for ONT to discontinue duplex cells on Nov 27 😅😂 Good thing Verkko also works great with HERRO-corrected simplex data!
📄 genome.cshlp.org/content/34/1...
📖 genome.cshlp.org/content/34/1...

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing https://genome.cshlp.org/content/early/2024/11/04/gr.279334.124 🧬🖥️

The BGA24 Logo

It's the 6-week countdown to The Biodiversity Genomics Academy 24, and we 30 fantastic and unique sessions!

You can join us at discord.gg/HBPytGx6sU to keep up to date with information and other attendees!

Session list: thebgacademy.org/BGA24/BGA24

#BGA24 #Bioinformatics #Biodiversity #Genomics

Complete genomes for the apes! We have added bonobo, chimp, gorilla 🦍, orangutan 🦧, and gibbon to the T2T family! Lots of very cool stories buried in these genomes, some of which we have explored here, but I expect many more studies to follow: www.biorxiv.org/content/10.1...

Animated GIF - Find & Share on GIPHY Discover & share this Animated GIF with everyone you know. GIPHY is how you search, share, discover, and create GIFs.

ModDotPlot preprint is now out! Winner of best poster at RECOMB 2023, it can generate either static or interactive dotplots in minutes using hierarchical modimizers. With @alexsweeten.bsky.social and @mikeschatz.bsky.social
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/marbl/ModDot...

Director, NIH Intramural Sequencing Center NHGRI seeks to identify an outstanding Director to lead its NIH Intramural Sequencing Center (NISC) within its Division of Intramural Research (DIR).

We are looking for a new director of the NIH Intramural Sequencing Center! Please spread the word: www.genome.gov/careers-trai...

10 years on, @bkille.bsky.social @treangen.bsky.social and co. have refreshed Parsnp with a version 2! Build a core genome multi-alignment for 100k SARS genomes or 1k Mtb genomes in under an hour 💨

Thanks for keeping an eye on my trophy for me.

Our new Center for Genomics and Data Science Research at NHGRI – which my own research group is now a part of – is seeking tenure-track or tenure-eligible investigators to join our program. Check out the ad and get your applications in by January 1! www.genome.gov/careers-trai...

GitHub - marbl/HG002: A complete diploid human genome A complete diploid human genome. Contribute to marbl/HG002 development by creating an account on GitHub.

We are excited to release v1.0 of our HG002 genome benchmark today! Our goal with the Q100 project is to create a complete and perfectly accurate representation of the diploid HG002 genome to serve as a replacement for current variant-based benchmarks. More info here: github.com/marbl/HG002

"The p-Arms of Human Acrocentric Chromosomes Play by a Different Set of Rules" An excellent review by Brian McStay on these newly completed regions of the human genome and why you should care: www.annualreviews.org/doi/abs/10.1...

Happy to move over, maybe I'll actually post on here unlike twitter.