iiinova — where your digital self keeps evolving

Reposted by Matt Holt

PacBio @pacbio.bsky.social · 07/10/2026

Planning your time at #ASHG26? Add #PacBio booth #605 to your list! Meet our scientists, see Revio & Vega in action, and explore how HiFi sequencing is helping researchers see more of the genome. Explore our full program: bit.ly/3TDejiN

041

Reposted by Matt Holt

PacBio @pacbio.bsky.social · 02/10/2026

#PacBio is headed to ASHG 2026 in Montréal! 🇨🇦 From complex variation to multiomic insights, see how HiFi sequencing is bringing more of the genome into view across human genomics. Discover what we have planned for #ASHG26: bit.ly/3TDejiN

042

Reposted by Matt Holt

Jocelyne Bruand @jocelyne8.bsky.social · 15/09/2026

Our Isocall paper is out on bioRxiv www.biorxiv.org/content/10.6...! 🎉 Isocall enables scalable joint isoform calling on PacBio data, allowing for the characterization of isoform diversity across cohort-scale data. (1/7)

174

Reposted by Matt Holt

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026

I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...

187109

Reposted by Matt Holt

Alex Spahn 🌋🌪️☄️ @spahn711.bsky.social · 28/08/2026

A quick edit of tonight's beautiful lunar #eclipse.

A close-up photo of the full Moon during a 96% lunar eclipse. The top of the Moon is bright white, but most of the rest is orange to red in color.

243152541

Matt Holt @holtjma.bsky.social · 27/08/2026

I'm basically all-in on noodles now except for "legacy" code! Even then, I've opportunistically lifted over a couple tools from rust-htslib, the LLMs help reduce that burden now.

020

Matt Holt @holtjma.bsky.social · 27/08/2026

Lastly, I want to make sure to thank my co-authors, our early testers, and our reviewers; all of which provided excellent feedback throughout this process! I’m glad we have such a great community for bioinformatics out there! 5/5

120

Matt Holt @holtjma.bsky.social · 27/08/2026

Lastly, the tool is blazing fast and easy to use! I’m personally very proud of how it turned out from a usability perspective. The tool is fully open source (github.com/PacificBiosc...), so give it a try if you’re doing benchmarking! 4/N

120

Matt Holt @holtjma.bsky.social · 27/08/2026

It turns out that BASEPAIR scoring is well-suited for both 1) evaluating variants that are represented differently and 2) providing a non-binary measure of accuracy. Both of these benefits make a big difference when evaluating variants in homopolymer or tandem repeat regions! 3/N

120

Matt Holt @holtjma.bsky.social · 27/08/2026

Aardvark is a tool similar to hap.py or vcfeval, where the goal measuring the accuracy of a call or "query" set against an established benchmark or "truth" set. Aardvark includes multiple scoring modes and introduces a unique "BASEPAIR" mode, which evaluates the variants at a sequence level. 2/N

110

Matt Holt @holtjma.bsky.social · 27/08/2026

Our article introducing Aardvark for variant benchmarking is now published in Genome Biology! “Aardvark: sifting through differences in a mound of variants” DOI: doi.org/10.1186/s130... GitHub: github.com/PacificBiosc... Follow along for some highlights… 1/N

doi.org

Client Challenge

12210

Reposted by Matt Holt

Ryan Hall, Y’all @rhyall.bsky.social · 25/08/2026

Thursday night, 96% of the Moon will disappear into Earth’s shadow. Most of the U.S. will be able to see it. One of the coolest sky events of the year.

04020

Matt Holt @holtjma.bsky.social · 20/08/2026

There are some situations where I absolutely love it, but I still get nervous whenever I have it touch a critical path in any piece of software. Fine toothed reviewing and testing whenever that happens…

010

Matt Holt @holtjma.bsky.social · 20/08/2026

Thanks, I was just trying to get a sense of ballpark speed and I think this does the trick! I have a mostly vibe-coded project (same fears you mentioned above) where I may be able to test a drop in replacement

110

Matt Holt @holtjma.bsky.social · 20/08/2026

I’ve generally defaulted to coitrees crate, any updated comparisons to that approach? (There was a dead link off the GitHub repo that may have hosted it)

100

Reposted by Matt Holt

Mayor Zohran Kwame Mamdani @mayor.nyc.gov · 18/08/2026

I'm listening, I'm learning. Safety first, NYC.

852345164420

Matt Holt @holtjma.bsky.social · 17/08/2026

Happy “GitHub is borked” day to those who celebrate!

010

Matt Holt @holtjma.bsky.social · 13/08/2026

Finally got around to beating Expedition 33… I was not emotionally prepared for the incredible journey of that game! 10/10, no notes

030

Reposted by Matt Holt

Dr. Lucky Tran @luckytran.com · 10/08/2026

Important: Trump’s executive order is NOT legislation. Though the executive order promotes more misinformation about vaccines, nothing has changed about the availability of childhood vaccines. For evidence-based guidance, please follow and share American Academy of Pediatrics recommendations.

3023001315

Reposted by Matt Holt

Nils Homer @nilshomer.com · 08/08/2026

When running benchmarks on shared tenancy systems (e.g. AWS), it's hard to compare cpu/wall times over time, even with many replicates. have seen performance differences up to 20% just based on fighting others for access to the memory sub-system.

121

Reposted by Matt Holt

Eric Topol @erictopol.bsky.social · 06/08/2026

Against all odds, with an HHS that has defunded mRNA research programs, the FDA just approved the first mRNA flu vaccine

452761583

Reposted by Matt Holt

Justice Of Toren One Var @jyn.dev · 05/08/2026

i'm really proud of this policy. it's not perfect, but i think it's close to the best that was possible given all the constraints. i'm excited that this will make things easier for mods and reviewers, and hopeful that it will spark change in Rust's governance. blog.rust-lang.org/inside-rust/...

blog.rust-lang.org

rust-lang/rust is adopting an LLM policy | Inside Rust Blog

Want to follow along with Rust development? Curious how you might get involved? Take a look!

1016724

Reposted by Matt Holt

Stephen Turner @stephenturner.us · 18/07/2026

How it started 👇... how it's going: blog.stephenturner.us/p/ai-dry-jul... Reflections on trying to go a month without AI. I made it two weeks (sort of).

blog.stephenturner.us

AI Dry July: Aborted

Reflections on trying to go a month without AI. I made it two weeks (sort of). 5.2k words, 23 minutes reading time.

0122

Reposted by Matt Holt

Randall Munroe @xkcd.com · 16/07/2026

Time Change xkcd.com/3272/

3-panel comic. (1) PERSON 1 behind podium on stage: We all hate springing forward. But we love falling back. (2) [Audience pictured listening] PERSON 1: Therefore, we are abolishing the *spring* time change *only*. We’ll gain an hour every year, but never lose one. (3) PERSON OFF-PANEL: Won’t that cause the clocks to spiral out of sync with the sun? PERSON 1 holding up a fist: *Then we will meet the chaos clear-eyed and well-rested!*

543739711

Matt Holt @holtjma.bsky.social · 15/07/2026

There is something cathartic about completing simple tasks

020

Reposted by Matt Holt

Adam Ameur @adameur.bsky.social · 03/07/2026

For those interested in PacBio's SPRQ-Nx chemistry and reusable SMRT Cells: in the Genome of Sweden project, we moved from 2 to 3 acquisitions per SMRT Cell in June. The results are impressive—we’re now approaching 400 Gb HiFi yield from a single SMRT Cell!

094

Reposted by Matt Holt

Alex Hoischen @ahoischen.bsky.social · 26/06/2026

Excited to share our ‘perspective’ on significant impact long-read sequencing technologies, genome assemblies and better (AI-assisted) interpretation-tools will bring to our field of medical genetics – as we are entering an era of “near-perfect genome sequencing”. www.nature.com/articles/s41...

nature.com

Near-perfect genome sequencing in medical genetics - Nature Genetics

This Perspective introduces near-perfect genome sequencing, which encompasses diploid genome assembly, pangenome references and artificial intelligence-driven variant interpretation, and proposes a ro...

163

Reposted by Matt Holt

Climate.us @climate.us · 23/06/2026

Climate.us is live. Built by members of the team behind Climate.gov, this new independent nonprofit website keeps trusted climate information easy to find, easy to use, and harder to erase. #ClimateForUs #ClimateUS

601549979

Reposted by Matt Holt

Fulcrum Genomics @fulcrumgenomics.com · 17/06/2026

@tfenne.bsky.social has a new post on tuning up bioinformatics’ old plumbing: HTSJDK, jlibdeflate, chelae, mako, GLIMPSE, verifyBamID, bwa-mem3, and the low-level tools behind everyday workflows. Improve the infrastructure. Validate the behavior. Let the gains compound. Blog post 👇

Bioinformatics runs on a hidden layer of shared infrastructure. samtools, GATK, Picard, htsjdk, Snakemake, Nextflow, and the libraries beneath them carry a huge share of day-to-day work. Most of it stays out of sight, like city plumbing.

271

Reposted by Matt Holt

PacBio @pacbio.bsky.social · 16/06/2026

One of the first preprints using the #PacBio Vega benchtop HiFi sequencer is now available. The study demonstrates accurate detection of mitochondrial heteroplasmy down to 1% using a single full-length mtDNA amplicon and applies the workflow to Parkinson's disease research. 🔗 bit.ly/4a4rP4c

031

Reposted by Matt Holt

Heng Li @lh3lh3.bsky.social · 16/06/2026

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

1193109

Reposted by Matt Holt

Rob Patro @robp.bsky.social · 14/06/2026

salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/

combine-lab.github.io

salmon

Fast, accurate transcript quantification from RNA-seq reads.

25316

Reposted by Matt Holt

Adam Ameur @adameur.bsky.social · 14/06/2026

These are beta test results of PacBio's reusable SMRT-cells, run on human blood DNA from the "Genome of Sweden" project. Results have been really impressive so far, with an average >250Gb per SMRT-cell over 2 acquisitions. We are now about to expand to 3 acquisitions

0114

Reposted by Matt Holt

Deborah Moine @deborahmoine.bsky.social · 12/06/2026

Excited to be heading to #ESHG2026 😃 If you're attending, feel free to stop by the #PacBio booth (420) and say hello. I'd be happy to chat about #PureTarget, HiFi sequencing, and targeted sequencing applications. If you're not attending ESHG, you can still catch this webinar on demand below.

032

Reposted by Matt Holt

Johannes Köster @johanneskoester.bsky.social · 12/06/2026

#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...

github.com

Release v4.0.0 · rust-bio/rust-bio

4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...

0197

Reposted by Matt Holt

PacBio @pacbio.bsky.social · 07/06/2026

Every bib represents a name, a loved one, or the entire rare-disease community. At the PacBio 5K on June 27, we carry them across the finish line together. 👟 Join us in Del Mar, San Diego and make your steps count. Sign up today: bit.ly/4mh0yQV #SeqItForward5K

031

Reposted by Matt Holt

Alex Hoischen @ahoischen.bsky.social · 04/06/2026

Congrats to all co-authors from out HiFi-Solves EMEA consortium! www.pacb.com/hifi-solves/ This study was driven particularly by the great @bartvds.bsky.social; with important contributions from Hanno Jörn Bolz Johannes Zschocke Malte Spielmann and their teams.

lnkd.in

This link will take you to a page that’s not on LinkedIn

253

Matt Holt @holtjma.bsky.social · 04/06/2026

How was the API lift? I haven’t had time to scope it yet

100

Matt Holt @holtjma.bsky.social · 02/06/2026

Following up on the major functional release of MethBat v1, we have had some more time to further optimize the tool and add some convenient features in v1.1. Run-time is *substantially* faster, especially if you're only looking for 5mC pileups! Update notes here: github.com/PacificBiosc...

020

Reposted by Matt Holt

Heng Li @lh3lh3.bsky.social · 30/05/2026

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

biorxiv.org

310944

Reposted by Matt Holt

Katie Mack @astrokatie.com · 29/05/2026

It’s truly astonishing to see how comprehensively the US government is tearing down every part of the system that has made it up until now a world-leading power in science, research, and technological development. The entire world will suffer from this wanton destruction.

23980442823

Matt Holt @holtjma.bsky.social · 27/05/2026

We released an update for HiPhase today that has a large impact on wall clock time required for some samples, with negligible differences in accuracy and block lengths. Full release here: github.com/PacificBiosc...

github.com

Release HiPhase v1.7.0 · PacificBiosciences/HiPhase

Changes Added a limit to the WFA edit distance that scales with the length of the mapping. This reduces run-time in regions with short mapped fragments and high edit distance relative to the refer...

000

Reposted by Matt Holt

Andrew Gallant @burntsushi.net · 26/05/2026

I've added an AI policy to ripgrep that was shamelessly copied from uv's policy. I plan to add this to the rest of my projects, but if anyone wants to offer feedback on wording, now would be a good time! github.com/BurntSushi/r...

github.com

611416

Reposted by Matt Holt

PacBio @pacbio.bsky.social · 26/05/2026

SPRQ-Nx chemistry is now shipping worldwide, bringing sub-$300 HiFi genomes to the Revio platform! This global rollout cuts sequencing costs by 30%, making it easier than ever to scale high-throughput workflows Full press release here: bit.ly/49HwmcL #SPRQNx #PacBio #HiFisequencing #Revio

0147