In honor of ASHG week, see “Choose your human genome reference wisely”(no paywall), in which Vivien Marx interviewed me on the state of the human reference genome. Vivien is always fun to chat with and I was in a slightly opinionated mood from the start — “The idea of a single reference genome is outdated,” says NIH researcher Adam Phillippy. Some of my other quotes follow with a little added context.
🚂 The T2T train keeps rolling. Our latest work investigating the structure and cause of Robertsonian chromosomes with the Gerton and Garrison labs is out today in the journal Nature! What’s a Robertsonian chromosome and why do they matter? More info below the break…
We are delighted to finally announce a preprint describing the Q100 project, where we finished the HG002 genome to near-perfect accuracy: A complete diploid human genome benchmark for personalized genomics
Join our team and contribute to the development of complete, personalized “telomere-to-telomere” (T2T) genome assemblies and the analysis of previously inaccessible regions of the genome! We are currently accepting applications for postbaccalaureate and postdoctoral researchers.
Today we published the complete “T2T” genomes of 6 ape species: chimp, bonobo, gorilla, Sumatran orangutan, Bornean orangutan, and siamang gibbon. This landmark resource is the result of a long-running collaboration (5 years of work!) led by myself, Kateryna Makova, and Evan Eichler. The genomes and our initial analyses are now presented in two papers: Complete sequencing of ape genomes published today, and The complete sequence and comparative analysis of ape sex chromosomes published last spring. There is a tremendous amount of data, code, etc. that goes along with this project, which we have organized on the T2T-primates project page. Don’t miss the T2T Browser Hub which presents all of this data as browser tracks, including expression, methylation, gene annotation, repeat annotation, etc. Comparing these genomes to our own furthers our understanding of human biology and genetic disease, including what makes us uniquely human, and brings us one step closer to understanding the language of the genome. I am excited to see what new discoveries will arise from these genomes!
We are excited to announce that Verkko2 is now available! Not only is it 4x faster than Verkko1, this version adds support for proximity ligation data (e.g. Hi-C, Pore-C) for T2T phasing and scaffolding without the need for trios. Our latest preprint describes the new methods and results: “Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding”. With these improvements, Verkko2 can now assemble, on average, around 40 out of 46 diploid human chromosomes as T2T scaffolds (and ~20 as T2T contigs), including the most difficult to assemble acrocentric chromosomes. However, these improvements are not limited to human genomes and Verkko2 should work well for any diploid or haploid genome (polyploids are a work in progress). We look forward to enabling many more T2T genomes in 2025!