Matt Holt
@holtjma.bsky.social
Staff scientist at @PacBio; formerly @hudsonalpha; avid gamer; opinions are my own
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/...
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!
blog.rust-lang.org
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).
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.
blog.stephenturner.us
Stephen Turner@stephenturner.us · 2mo agoI'm going to try something next month. AI deskilling is real. I'm going a month without it. blog.stephenturner.us/p/ai-dry-july
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!
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...
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...
nature.com
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
Rust and python bindings for minibwa are available on crates.io and pypi.org: github.com/fg-labs/mini...
GitHub - fg-labs/minibwa-bindings: Rust and Python bindings for minibwa — Heng Li's lightweight bwa
Rust and Python bindings for minibwa — Heng Li's lightweight bwa - fg-labs/minibwa-bindings
github.com
@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 👇
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
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
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/
salmon
Fast, accurate transcript quantification from RNA-seq reads.
combine-lab.github.io
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
PacBio@pacbio.bsky.social · 2mo agoSharing results from a beta test of PacBio’s SPRQ-Nx reusable SMRT cells using two acquisitions! This increased SMRT cell throughput reduces sequencing costs for large human WGS projects. #ESHG2026 #PacBio #ESHG
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.
PacBio@pacbio.bsky.social · 2mo agoRepeat expansions and other complex genomic regions continue to challenge traditional sequencing workflows. 🎥 Hear how Dr. Maximilian Thelen is using PureTarget™ HiFi sequencing for repeat expansion analysis and custom panel development. Watch the recording: bit.ly/3S1axP5 #PureTarget
#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...
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...
github.com
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
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.
This link will take you to a page that’s not on LinkedIn
lnkd.in
The American Journal of Human Genetics@ajhgnews.bsky.social · 2mo ago🧬New from @ahoischen.bsky.social & co! 📄HiFi sequencing accurately identifies clinically relevant variants in paralogous genes
🧬New from @ahoischen.bsky.social & co! 📄HiFi sequencing accurately identifies clinically relevant variants in paralogous genes
HiFi sequencing accurately identifies clinically relevant variants in paralogous genes
Long-read HiFi genome sequencing combined with Paraphase enables comprehensive detection of all clinically relevant variant types in paralogous genes. It resolves “dark” regions while enabling haploty...
cell.com
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...
Matt Holt@holtjma.bsky.social · 3mo agoWe had a *major* update to MethBat v1 today in preparation for SPRQ-Nx release. This included a `pileup` sub-command for 5mC, 5hmC, and 6mA and extension of the existing functionality to support the additional base mods. Full notes here: github.com/PacificBiosc...
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
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.
Dan Vergano@danvergano.bsky.social · 2mo agoWhite House proposes new rules giving political appointees final approval of research grants These proposed Office of Management and Budget regulations would render the federal research grant review process opaque www.scientificamerican.com/article/whit...
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...
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...
github.com
In case you don't follow it already, reminder that this exists! scientificcomputing.rs/monthly/
Scientific Computing in Rust
the Scientific Computing in Rust annual workshop and monthly newsletter.
scientificcomputing.rs
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
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
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
n.pr
We had a *major* update to MethBat v1 today in preparation for SPRQ-Nx release. This included a `pileup` sub-command for 5mC, 5hmC, and 6mA and extension of the existing functionality to support the additional base mods. Full notes here: github.com/PacificBiosc...
I’m sorry but if you aren’t sure of a citation, whether what it means or that it exists… why are you citing it. why are you referring to something you haven’t read or don’t understand? that defeats the entire bloody point
Dr. Holly Walters@manigarm.bsky.social · 3mo agoI'm sorry, what? In writing my first monograph, I spent six weeks trying to track down a citation in TWO languages I didn't know. And good thing too, because the citation was wrong. That's scholarship. That's research. You know, the thing we're trained to do?!?
1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius
The immediate action by so many states to make gerrymandering worse reveals just how awful of a ruling the SC made. Minorities will suffer most because of this.
Stephen Wolf@stephenwolf.bsky.social · 3mo agoAlabama’s lieutenant governor, who also serves as president of the state Senate, posted a 7-0 Republican gerrymander calling for his party to eliminate both Black Democrats. Every seat on a map like this would be dark red and heavily white
![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!*](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreidl5ovrvqzuhtr6ygqwtdjes2qraloyxtxqrvjwu7xxxersawskde)