iiinova — where your digital self keeps evolving

Reposted by Andrew Carroll

Guillaume Holley @guillaumeolesan.bsky.social · 20/08/2026

I am delighted to present with @hannespetur.bsky.social our new study on the Icelandic pangenome reference HPRC-ICE. This work goes all the way from pangenome construction to disease association! (1/7) www.nature.com/articles/s41...

nature.com

An Icelandic pangenome reference - Nature

Newly developed methods enable construction of Icelandic haplotypes and mapping of population-scale short reads to a pangenome by reducing reference bias and improving discovery in low-mappability reg...

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Andrew Carroll @acarroll.bsky.social · 01/07/2026

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...

andrewcarroll.github.io

The Best of Both Worlds - Assessing MiniBWA

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

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Andrew Carroll @acarroll.bsky.social · 28/05/2026

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...

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Andrew Carroll @acarroll.bsky.social · 07/03/2026

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...

github.com

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...

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Reposted by Andrew Carroll

Chris Saunders @ctsa.bsky.social · 20/02/2026

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)

Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.

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Andrew Carroll @acarroll.bsky.social · 10/02/2026

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...

andrewcarroll.github.io

For Automation The Wet Lab Has An Incredibly Long Tail

Disclaimer: These are solely my views.

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Reposted by Andrew Carroll

Vertebrate Genomes Project @vertebrategenomes.bsky.social · 03/02/2026

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...

African penguin
Source: Wildlife Conservation Society

Cotton top tamarin
Source: Wildlife Conservation Society

Eld's deer
Source: Wildlife Conservation Society

Elongated tortoise
Source: Wich’yanan (Jay) Limparungpatthanakij, via inaturalist.org and Wikimedia Commons

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Andrew Carroll @acarroll.bsky.social · 03/02/2026

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...

blog.google

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.

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Reposted by Andrew Carroll

Barack Obama @barackobama.bsky.social · 25/01/2026

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.

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Andrew Carroll @acarroll.bsky.social · 24/12/2025

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...

andrewcarroll.github.io

The Virtual Cell Will Be More Like Gwas Than Alphafold

There has been significant discussion recently on the concept of the “virtual cell.” I want to summarize the key concepts regarding what the field wants from a virtual cell and the challenges we face....

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Reposted by Andrew Carroll

Joseph Guhlin @josephguhlin.bsky.social · 28/10/2025

🐧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

Hoiho - the world’s rarest penguin, fewer than 150 mainland pairs left

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Reposted by Andrew Carroll

Stephen Turner @stephenturner.us · 16/10/2025

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...

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Reposted by Andrew Carroll

Adam Phillippy @aphillippy.bsky.social · 22/09/2025

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]

biorxiv.org

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 ...

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Andrew Carroll @acarroll.bsky.social · 21/08/2025

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.

go.roche.com

Germline Small Variant Calling Workflow for SBX Duplex Data

Wednesday, September 10, 2025 at 12:00 PM Eastern Daylight Time.

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Andrew Carroll @acarroll.bsky.social · 13/05/2025

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...

github.com

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...

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Reposted by Andrew Carroll

Adam Keiper @adamkeiper.com · 02/02/2025

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."

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Andrew Carroll @acarroll.bsky.social · 05/12/2024

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...)

Runtime figure for new version of DeepVariant with and without small model. Showing reduction in runtime of 155 minutes to 101 minutes with Illumina, 174 minutes to 71 minutes with PacBio, and 295 minutes to 114 minutes with Oxford Nanopore.

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Andrew Carroll @acarroll.bsky.social · 26/10/2023

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...

github.com

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...

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Reposted by Andrew Carroll

Mikhail Kolmogorov @mishakolmogorov.bsky.social · 24/10/2023

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...

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Andrew Carroll @acarroll.bsky.social · 24/10/2023

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.com

GitHub - google/deepsomatic

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

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Reposted by Andrew Carroll

Alex Rubinsteyn @alexr.bsky.social · 14/09/2023

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. 🧪🧬🖥️🔬

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