GRCz12tu is available on Genbank. This will be one of two genomes that will be considered "reference" genomes, there will also be a GRCz12ab assembly coming. It has entered the NCBI annotation pipeline and will also go into the Ensembl annotation pipeline. www.ncbi.nlm.nih.gov/datasets/gen...

A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation https://www.biorxiv.org/content/10.1101/2025.02.24.639687v1

This is becoming a tradition! We are inviting students and postdocs broadly interested in computational cancer to 2025 NCI Spring School on Algorithmic Cancer Biology. Happening Mar 10-14. Please apply and spread the word: ncifrederick.cancer.gov/events/confe...

Why was @sexchrlab.bsky.social in snowy Bethesda today? Big news coming later this month! Stay tuned… 🧬

Kateryna Makova and I have a new preprint out on non-canonical DNA in human and ape T2T genomes: www.biorxiv.org/content/10.1... Collaboration with Kaivan Kamali, Francesca Chiaromonte, Eduard Kejnovsky, and Iva Kejnovska. Graphical abstract by Dani Zemba.

T2T-F2F 2024 is a wrap! Great to hear about the new discoveries being enabled by complete genomes, and to meet so many new, enthusiastic T2T’ers. Thanks for the great meeting @khmiga.bsky.social @ucscgenomics.bsky.social !! 🎉

We welcome you to join us for the T2T Consortium Face-to-Face (T2T-F2F) Meeting in Santa Cruz, CA 9/2-3. Open to all -- register today.🏄‍♀️ sites.google.com/ucsc.edu/t2t...

We demonstrate a single-platform solution for complete T2T genomes on the ONT PromethION: Duplex + Ultra-long + Pore-C, aka "TNT" 🧨 Expecting rapid improvements in the coming year. Congrats @sergek.bsky.social @zbao.bsky.social @awngs.bsky.social @awngs.bsky.social @khmiga.bsky.social et al.!

We find that 12 of the 13 WASHC1 paralogues are likely to be pseudogenes, and that the only functional WASHC1 gene is on chromosome 20, not on chromosome 9 as was previously thought. This goes some way to explaining why so little is known about this vital gene, an integral part of the WASH complex.

Congrats!! 👏👏 👏 This is an important piece demonstrating paralogous genes newly found in T2T-CHM13 better represents the coding form while the version in hg38 that was conceived as protein coding turned out to be a pseudogene. Also supported by the #HPRC assemblies. #T2Tgenomes

Rewriting regulatory DNA to dissect and reprogram gene expression https://www.biorxiv.org/content/10.1101/2023.12.20.572268v1

Cell type specific enrichment of somatic aneuploidy in the mammalian brain https://www.biorxiv.org/content/10.1101/2023.12.18.572285v1

If you're looking to do long-read sequencing, Katy's awesome!

Pleased to see the Y in here. Full credit for the Y rhyming AI to make it into the title!

Last week we also released updated T2T assemblies for the autosomes as well! Species include: chimp, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang gibbon. These are making their way to GenBank, but see here for a preview: github.com/marbl/Primates Lots more analyses to come!

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes https://www.biorxiv.org/content/10.1101/2023.11.30.569198v1

What happens when cluster goes down for maintenance. Counter clockwise: @sergek.bsky.social @nancyfhansen.bsky.social @juhyunk.bsky.social @aphillippy.bsky.social playing. @pickettbd.bsky.social taking a break.

Come work with us 🙂

NCI Spring School on Algorithmic Cancer Biology is happening again Apr 1-5 2024! The registration is now open, we invite trainees broadly interested in computational cancer biology to participate. Please apply and spread the word! ncifrederick.cancer.gov/events/confe...

Tandem repeats are hard! Get your benchmark from @genomeinabottle.bsky.social to compare caller : biorxiv.org/content/10.1... 1.7 mil TR catalog; new tooling to overcome variant representation issues (SNV &SV); insight in complexity. First time we can compare across different techs/caller!

New preprint out from #NIST in collaboration with @sexchrlab.bsky.social tackling variant calling on the X and Y chromosomes in the human T2T assembly! www.biorxiv.org/content/10.1...

The complete human diploid reference genome of RPE-1 identifies the phased epigenetic landscapes from multi-omics data https://www.biorxiv.org/content/10.1101/2023.11.01.565049v1

NHGRI is searching for new faculty in computational genomics! The NIH intramural program funds labs, not projects, so it's all research and no grant writing. Come work with me at one of the best places in the world to do genomics research! #ASHG23 www.genome.gov/careers-trai...

Fixed it!

Y chromosome team reunion with Charles and Pille! #ASHG23

We are excited to release v1.0 of our HG002 genome benchmark today! Our goal with the Q100 project is to create a complete and perfectly accurate representation of the diploid HG002 genome to serve as a replacement for current variant-based benchmarks. More info here: github.com/marbl/HG002

Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline github.com/KolmogorovLa...

Initial release of DeepSomatic, which identifies subclonal variants when given tumor and normal BAM files. Pre-trained models and case studies available for Illumina and PacBio. Development led by Kishwar Shafin which built off a framework by Pi-Chuan Chang. (github.com/google/deeps...)

Kateryna Makova and I were excited to be guests on Science Friday to discuss the Y chromosome. Congrats to the amazing @arhie.bsky.social, Sergey Nurk, and others on completing this last unfinished chromosome! Tune in here if you’re curious about ChrY: www.sciencefriday.com/segments/y-c...