🎉 It's published! Our placental long-read transcriptome is now in @natcomms.nature.com! Thank you to @arjunbhattac.bsky.social, @jonhuang.bsky.social, and @mikelove.bsky.social for collaborating on this first project of my postdoc @mdanderson.bsky.social. A recap 🧬🫄🧵 www.nature.com/articles/s41...

Huge thank you to @plbaldoni.bsky.social & @robp.bsky.social for InfRV tools, and collaborators across Singapore, Canada & USA. Also to coauthor (and talented undergrad at Rice U BioSciences) Aryun Nemani for a lovely Shiny app for our visualizing our assembly seantbresnahan.com/lr-placenta-...

Huh?! RustQC and RastQC both released within hours of each other? bsky.app/profile/bior...

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀 I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵 seqeralabs.github.io/RustQC/

Happy Birthday @benlangmead.bsky.social!

Typst Books, Article Layout, and typst-gather quarto.org/docs/blog/po...

Looking forward to it!

The past few streams have been pretty high level, but not this time! Friday at 4p UTC (everytimezone.com?t=69cf0300,3c0), we're going back down to "what bits go where". We'll try to write an audio generator that produces WAV files with white/pink/brown noise by hand 🔊 youtube.com/live/BKHE7st...

If you use our fgbio UMI tooling today, you owe it to yourself to check out fgumi! Massively faster re-write into Rust by @nilshomer.com with 100% reproduction of the fgbio outputs!

@robp.bsky.social you were asking a few weeks ago for AI rust porting examples. Here's probably our biggest to-date. All the UMI tooling from fgbio. @nilshomer.com invested a lot of time into this beyond straight porting (e.g. massively better concurrency in many areas).

Hash tables, or how to leverage the sinking feeling of loneliness you get when you look at the sky

We’ll be sharing a detailed blog post in the coming days with everything that was built, discussed, and what comes next. Stay tuned 🚀

What stood out most was how naturally these efforts connect back to the broader vision of scverse: building a unified, extensible ecosystem for all things single-cell A big thank you to our sponsors who made this possible: 10x Genomics, Biohub, Proteintech, Lamin, and Pfizer.

Two inspiring days in Berlin just wrapped up with our scverse hackathon on single-cell and spatial proteomics and it’s hard not to feel energized by what this community can do together.

Is there a German word for the particular type of schadenfreude one feels watching the stock of RAM manufacturers plummet after OpenAI backed out of their deal to buy 41% of the global RAM supply?

Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish https://www.biorxiv.org/content/10.64898/2026.03.25.714356v1

The people who believe that generative AI development & adoption everywhere is the ultimate goal & the first order predictor of success are insufferable. So are the people who think that AI can't ever produce anything useful and that everything they do produce is "slop". I miss reasoned arguments.

After looking for a while, it seems that no @10xgenomics.bsky.social Flex v2 data is actually publicly available right now! If you have Flex v2 data that you’d be willing to share for testing / tool development purposes, please reach out to me!

I feel like @biorxivpreprint.bsky.social is on whatever scaling infrastructure @anthropic.com is using — they both seem to be down / have degraded service _a lot_ recently.

just ... so on the nose.

New desktop workstation; who dis?

Simpleaf 0.23 out now; you can now output your multiplex quantification directly as an AnnData object, along with all of the relevant metadata for downstream processing and QC! Check it out on bioconda!

One of the amazing benefits to me, having moved our entire single-cell stack over to Rust (from a combination of Rust & C++), is that I can develop on one machine (my MacOS M1 Max) and have the tools build seamlessly across MacOS and Linux, x86 and ARM. The compilation on other platforms just works!

And already an important update / improvement to multi-sample probe-based quantification (i.e. Flex) ;P. bsky.app/profile/robp...

Made some updates to the generality of multi-sample probe quant (i.e. previously flex-quant, now multiplex-quant) in simpleaf/alevin-fry. The correlations on the Flex v1 data look... pretty convincing. New stack needs piscem 0.18, alevin-fry 0.13 & simpleaf 0.22 (last one still waiting on bioconda).

Made some updates to the generality of multi-sample probe quant (i.e. previously flex-quant, now multiplex-quant) in simpleaf/alevin-fry. The correlations on the Flex v1 data look... pretty convincing. New stack needs piscem 0.18, alevin-fry 0.13 & simpleaf 0.22 (last one still waiting on bioconda).

This is a really interesting thread, and I agree with a lot of the points in it. However, I think it's critical to separate the *technical* "agentic coding skeptic" position from the *effect/outcome/ethical* "agentic coding skeptic" position. The former is a much less tenable position, IMO.

This is a very real ducking win!

We're looking for a publicly available 10x Flex v2 gene expression dataset to test out our simpleaf pipeline on (we need raw FASTQ data and, ideally, CellRanger count matrices). Unfortunately, 10x only has Flex v1 data available on their website, and the v2 chemistry is different. Any ideas?

10x Flex Gene expression support is now part of the piscem -> alevin-fry workflow, and also has a nice, low-friction command in simpleaf! Check out the tutorial here (combine-lab.github.io/alevin-fry-t...). This was a major feature upgrade, so we're looking for testers and feedback :).

Big feature upgrade in the piscem/alevin-fry/simpleaf ecosystem—10x Flex gene expression support in the just-released piscem 0.17.1, alevin-fry 0.12, simpleaf 0.21! This heavy lift required adding support for hierarchical barcoding (among other feats). We're looking for feedback; please try it out!

Piscem now supports reads with both sample-level and cell-leval barcodes github.com/COMBINE-lab/... : the corresponding changes in alevin-fry and simpleaf are incoming :). Want an easy path (rather than a complex workflow) to 10x Flex gene expression in alevin-fry, you got it!

Went looking for a full-stack GA4GH refget implementation in Rust. Couldn't find one, so I had Claude build it. 🦀 refget-rs server, client, data models, storage, & CLI for Sequences v2.0.0 + Sequence Collections v1.0.0. Serve, query, compare, compute digests. 🔗 github.com/fulcrumgenomics/refget-rs

I finally wrote up a paper for perbase! The process with @joss-openjournals.bsky.social was really great! github.com/sstadick/per...

Sassy2: Batch Searching of Short DNA Patterns www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/RagnarGrootK...

We have lost so many potential scientists. That loss compounds geometrically over time. We have lost leading scientists who would have come to the US from their home country, & we are losing leading scientists born here who will not go into science because this admin has made it a public target.

Very happy that I got the order in on the new lab server with 1.5TB of RAM a bit ago. Still waiting on delivery, but locking down the price turned out to be a big win!

This is very cool! I remember talking through GitHub issues very early on with Will & I'm happy to see what they've built all this time later :). As a tool developer, I can't overstate the importance of having users willing to give you feedback, suggestions & find weird edge cases! Congrats!

New preprint! Our workflow for processing single cell and nuclei data, called 🎉 scprocess 🎉 We have been working on it for ~18 months now, over which time we have processed at least 2k samples with it, so it has had a decent amount of testing.

scprocess: a pipeline for processing, integrating and visualising atlas-scale single cell data #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.03.09.710141v1

Icefish: Practical zk-SNARKs for Verifiable Genomics (Alexander Frolov, Maurice Shih, Rob Patro, Ian Miers) ia.cr/2026/463

scprocess: a pipeline for processing, integrating and visualising atlas-scale single cell data https://www.biorxiv.org/content/10.64898/2026.03.09.710141v1

Sassy2: Batch Searching of Short DNA Patterns https://www.biorxiv.org/content/10.64898/2026.03.10.710811v1

BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing https://www.biorxiv.org/content/10.64898/2026.03.12.706999v1

It's a good day when the first item in your feed is your own work :) @rickbitloo.bsky.social was annoyed that scanning reads for all 96 rapid kit barcodes is bottleneck in Barbell, so he made Sassy2: 13x (150bp) to 4.6x (8kbp) faster than v1 by batch-searching patterns, and >100Gbp/s on 16 threads!

Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv. docs.google.com/document/d/1...

Congratulations, @vikramshivakumar.bsky.social!

I've been wanting to do a big refactor and build system update for salmon for a looong time. I finally got around to it, and updated the backend index to use the newest SSHash while I was at it : github.com/COMBINE-lab/... (also with native ARM support & on bioconda!)

This is a false trichotomy.

Sad news, but what a long and incredible life!