🐧We researched one of the world’s rarest #penguins. The yellow‑eyed penguin (aka hoiho/takaraka) isn’t one homogeneous species after all!

www.biorxiv.org/content/10.1...

#hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature

Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic www.nature.com/articles/s41... (read free: rdcu.be/eLny0) github.com/google/deeps...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

I'll be speaking in this webinar (go.roche.com/sbx-d) on September 10, where I'll share our benchmarks and observations for Roche's SBX sequencing instrument, as well as models developed by our team for SBX data.

Release of DeepVariant and DeepSomatic v1.9

DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).

DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.

github.com/google/deepv...

Incredibly moving Justin Trudeau remarks:

"We have fought and died alongside you....During your darkest hours...we were always there. Standing with you, grieving with you, the American people....Canadians are a little perplexed as to why our closest friends and neighbors are choosing to target us."

Release of DeepVariant 1.8. Large speed improvement (~67% faster) via small model for easy sites. New Pangenome-aware option. Reduces error by ~30% for vg-mapped WGS, ~10% for BWA WGS, ~5% BWA exome. New config for custom model users, see release notes.

(github.com/google/deepv...)

How do we make a pangenome maximally relevant for the study of a new sample? www.biorxiv.org/content/10.1...

Release of DeepVariant v1.6.

Support for haploid regions, chrX/Y.
Workflow for Pangenome FASTQ-to-VCF.
Major DeepTrio improvements for de novo variants.
Models for CompleteGenomics T7, G400
Add NovaSeqX to training data

Release by Kishwar Shafin

github.com/google/deepv...

Proud of Ayse Keskus and Asher Bryant in my group for making this happen! This work is a collaboration with Children's Mercy, UCSC and Google Health - who are also releasing the first version of DeepSomatic today: github.com/google/deeps...

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...)

Best resource for getting extracellular domain localization from Ensembl gene/protein IDs?

I tried the subcellular locations in HPA but the membrane annotation is mostly fully intracellular proteins.

🧪🧬🖥️🔬