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!

Last year we released complete, gapless, “T2T” sex chromosomes for chimp, bonobo, gorilla, Sumatran orangutan, Bornean orangutan, and siamang gibbon. This December we are proud to announce our latest preprint “The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes”! Over the past year, we have also finished the autosomes for these genomes! The v2.0 assemblies for these species are now available from our T2T-primates project page, and all of the raw HiFi, ONT, Hi-C, and Illumina sequencing data can be found on GenomeArk. This has been a Herculean effort involving nearly everyone in the lab and a large swath of the T2T team. It turns out that finishing six genomes is a lot more work than finishing one! A huge thank you to everyone involved, especially Kateryna Makova for spearheading the project.

Today, we are excited to release the v1.0 T2T assembly of the HG002 benchmark genome! This assembly is part of what we have dubbed the “Q100” project, or in other words, our quest to assemble a completely error-free human genome (in the Phred QV scale, Q100 equates to an error rate of 1 per 10 billion bases). The Genome in a Bottle consortium has released some tremendous resources over the years, including DNA reference materials such as HG002. However, these reference materials are currently defined as a list of variants called against the GRCh38 reference genome. A more natural representation is the complete sequence of the genome itself, i.e. a “genome benchmark” as opposed to a “variant benchmark”. This is our first step towards creating such a genome benchmark. We will have much more to say about this in the coming year, but for now you can find more information at the GitHub page linked above.

Our latest paper, with the self-explanatory title The complete sequence of a Y chromosome, is now published! If you do not have a Nature subscription, here is a free-to-read link. This complete Y chromosome marks the final human chromosome to be finished from telomere to telomere, and its sequence has been incorporated into the CHM13v2 reference genome, which now includes the complete sequence of all 24 human chromosomes. The complete sequence and associated analysis resources can be found on the CHM13 GitHub repo. Congrats to the entire T2T team on completing this highly repetitive chromosome that was once considered “unassemblable”!