Thread by @_johntlovell

We've been exploring the new #T2T human genome assembly compared to previous versions (our news and views article is out today, link below). Some observations:
(1) Its pretty amazing what the human genome project was able to do in 2004: large-scale gene order is totally conserved

(2) Some of the chromosomes are nearly identical between the 2013 GRCh38 assembly and T2T. For example, here is a zoom in on Chr10 - just a few gaps in the pericentromere that were filled in with tandem repeats in T2T.

(3) But other chromosomes have been dramatically improved. For example, here are Chr9 and acrocentric Chr14.
Plot legend: sliding window proportion of sequence in genes (dark orange = exons) and repeats (light blue = #repeatMasker, dark blue = #trf); red segments = GRCh38 gaps.

I'm happy to post figs for other chromosomes - let me know what you want to see, and I'll add them to this thread.

Figures made with #GENESPACE (github.com/jtlovell/GENES…) and #ggplot2.

Jane Grimwood and I have put together a short "news and views" about the impacts of the T2T genome. Find it here: nature.com/articles/d4158…

The main telomere-to-telomere paper was published earlier this year: science.org/doi/10.1126/sc…. The new v2 T2T genome with the complete Y chromosome is now on NCBI.
*I was not involved in the T2T publication or data generation, just excited to see it out!*

Per @stncsn's request, here is Chr6. One of the cleanest chromosomes in the GRCh38 assembly.

@EalesJames, the Y has to be the most improved of all the chromosomes. Comparative genomics with both sex chrs is going to open some really exciting lines of inquiry.