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It's finally finished!

March 31, 2022

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!

We are hiring!

October 27, 2021

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.

The (near) complete sequence of a human genome

September 22, 2020

The Telomere-to-Telomere (T2T) consortium is proud to announce our v1.0 assembly of a complete human genome. This post briefly summarizes our work over the past year, including a month-long virtual workshop in June, as we strove to complete as many human chromosomes as possible. Our progress over the summer exceeded our wildest expectations and resulted in the completion of all human chromosomes, with the only exception being the 5 rDNA arrays. Our v1.0 assembly includes more than 100 Mbp of novel sequence compared to GRCh38, achieves near-perfect sequence accuracy, and unlocks the most complex regions of the genome to functional study. We plan to release a series of preprints in the coming months that fully describe our methods and analyses, but due to its tremendous value, we are releasing the assembly immediately.

De novo assembly of haplotype-resolved genomes with trio binning

October 22, 2018

Our latest paper with Tim Smith (USDA) is now out in Nature Biotechnology — “Complex allelic variation hampers the assembly of haplotype-resolved sequences from diploid genomes. We developed trio binning, an approach that simplifies haplotype assembly by resolving allelic variation before assembly … Trio binning uses short reads from two parental genomes to first partition long reads from an offspring into haplotype-specific sets. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction.” Here are links to the full paper and a nice summary from NHGRI with quotes from me and Tim. Credit to Sergey Koren and Arang Rhie for developing this great new method. We have many more trios planned!

Human genome assemblies with nanopore, an update

May 23, 2018

We recently participated in a collaborative effort to sequence, assemble, and analyze a human genome (GM12878) using the Oxford Nanopore MinION (Jain et al. 2018). Since then, we’ve also developed a trio-based strategy for assembling complete haplotypes from long-read data (Koren et al. 2018). Oxford Nanopore has continued to advance in the meantime, releasing several major base-calling updates. Other tools, such as Nanopolish, have also gotten faster and added new functionality, like methylation-aware polishing. So, we decided to re-analyze the dataset from the paper using the latest base calling and assembly tools. The new assembly increases the NG50 to over 10 Mbp and trio binning accurately reconstructs key MHC genes for both haplotypes.

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