How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

This blog shares some thoughts on protein and genome foundation models. The first part explains some of the concepts by training models for example tasks. The second part is opinion on the state of the field. andrewcarroll.github.io/2026/05/26/g...

Release of DeepVariant v1.10 Phased VCF output for long-reads Accuracy improvements for multi-allelic variants Pangenome accuracy improvements (18% fewer errors) Most technologies ~10% faster RNA-seq is a full supported mode DeepSomatic is 12-40% faster github.com/google/deepv...

Release DeepVariant 1.10.0 · google/deepvariant

DeepVariant: Continuous phasing: Long-read variant calls (PacBio and ONT) are now natively phased and phased output is generated for both vcf and gvcf formats. Fuzzy channels: Added “fuzzy channel...

github.com

What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)

Lab tour and takeaways: www.youtube.com/watch?v=nS2o...

The "Why Not?" Era of Sequencing Has Begun

YouTube video by OMGenomics

youtube.com

I wrote up some thoughts on the automation of lab work, in particular how it relates to how people will work in the lab. In short, it will deliver a lot of value for assays run at scale, but there is a long tail of experiments where humans are essential. andrewcarroll.github.io/2026/02/09/f...

Thanks to the support of @wcs.org and Google Research, we have sequenced and assembled the genomes of nine endangered species, with more on the way! To learn more: blog.google/innovation-a...

This blog talks about the great work of the @ebpgenome.bsky.social. To support it Google.org has funded sequencing and open release of 13 genomes, with a $3M commit to sequence 150 more and develop methods to improve assembly finishing and other bottlenecks. blog.google/innovation-a...

How we’re helping preserve the genetic information of endangered species with AI

Scientists are working to sequence the genome of every known species on Earth.

blog.google

The killing of Alex Pretti is a heartbreaking tragedy. It should also be a wake-up call to every American, regardless of party, that many of our core values as a nation are increasingly under assault.

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful. andrewcarroll.github.io/2025/12/23/t...

🐧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]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

biorxiv.org

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...

Release DeepVariant 1.9.0 · google/deepvariant

DeepVariant: In this version we have updated our training scheme for the HG002 sample with the newly released HG002-T2T truth set which improves accuracy against that truth set. Our labeling metho...

github.com

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...

Personalized Pangenome References

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org

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...

Release DeepVariant 1.6.0 · google/deepvariant

Improved support for haploid regions, chrX and chY. Users can specify haploid regions with a flag. Updated case studies show usage and metrics. Added pangenome workflow (FASTQ-to-VCF mapping with V...

github.com

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...)

GitHub - google/deepsomatic

Contribute to google/deepsomatic development by creating an account on GitHub.

github.com

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. 🧪🧬🖥️🔬