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 center coordinator, bioinformatics engineer/scientist, and postdoctoral researcher.
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”!
Today is a big day. One that was 30+ years in the making. We have finally uncovered every last bit of the human genome! I wanted to celebrate by writing a behind the scenes tribute to the amazing members of the T2T consortium, but that will have to wait. The past two years have been a whirlwind and I need some time to recuperate. For now, just the basics: links to the assembly, the browser, and the papers. And don’t worry, we didn’t forget chrY this time!
Update: These positions have now been filled The Genome Informatics Section is hiring! Come join our outstanding team at the NIH’s National Human Genome Research Institute and contribute to the development of new reference genomes and computational methods for DNA sequencing and analysis. Will consider postdoc, PhD, and engineer applications. More information and application instructions follow below.