Start from the patient, name the real gap, then build the analysis that closes it. @fulcrumgenomics.com VP of Translational Research Juliann Chmielecki, PhD nails it. Worth your time if you work anywhere near translational oncology. www.linkedin.com/pulse/from-e...

unum: a pure-Rust HLA/KIR genotyper It's a port of github.com/mourisl/T1K, offering significant speedups, ergonomics, and opinionated improvements. I am looking for folks who want to give it a try and give constructive feedback. github.com/fg-labs/unum

🚀 ferro-hgvs 0.7.0 is out: our biggest release yet. Major upgrades to HGVS normalization, parsing & projection: spec-compliant 3′ shifting, mosaic/compound alleles, multi-axis projection (g/c/n/p/r), Ensembl support, plus ~1.7× faster parsing. github.com/fulcrumgenom...

Save the compute, save the world!

Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg

#bioinformatics re-writes are more often about doing it "right" this time, rather than faster this time. #genomics #rust #rewrites

New riker release this morning - version 0.4.0 is out! Major updates are: - New "rna" tool that ports picard CollectRnaSeqMetrics, fgbio EstimateRnaInsertSize, and much more - New global --threads option to multithread input BAM/CRAM decoding - Big performance improvements in "wgs" and "hybcap"

🚀 bwa-mem3 v0.5.0 is out 🎉 One flag to rule them all. The new --fast preset makes whole-genome alignment ~2× faster while preserving accuracy and recall. 🧵 github.com/fg-labs/bwa-...

New on the Fulcrum blog: minibwa, a faster mapper from @lh3lh3.bsky.social and our @nilshomer.com Its speed is great, yes, but more interesting is the decision to revisit BWA-MEM as infrastructure – keep what still works, change what limits performance, then test downstream impact. shorturl.at/xxqeI

Hey @nilshomer.com, you'd asked about this in the past: we finally got around to implementing byte-level determinism in salmon (github.com/COMBINE-lab/...). It turned out to require a lot of thought and changes, but it turns out we can do it elegantly (with RAD files) and fast (`--deterministic`)!

re-writes aren't just about speed dupblaster, riker, chelae, and methylsieve: the stack is being re-written, not just faster, but with the fixes we've always wanted

Realized that I released a couple of new tools last week and didn't announce anything. The first one is *dupblaster*. Samblaster inspired streaming queryname grouped duplicate marking for NGS reads: github.com/fulcrumgenom...

minibwa + ALTs: github.com/nh13/minibwa... In-mapper ALT-aware MAPQ recovery via DRAGEN-style liftover groups. No bwa-postalt.js. Matches bwa+postalt, byte-identical without a .alt file. Works how I want it to. The real test will be when others give it a try. No warranty, implied or otherwise.

🚀 new bwa-mem3 is out. Why use it? - 🏛️keep using a bwa-mem variant (avoid revalidation/reprocessing) - 🚅 1.7x faster/20% less memory than bwa-mem2 - 🧬native methylation support (asymmetric scoring) - ✅ matches bwa-mem2 output - 👊opt-in knobs to go even 2x faster bwa-mem3.readthedocs.io/en/latest/

Rust and python bindings for minibwa are available on crates.io and pypi.org: github.com/fg-labs/mini...

Faster samtools sort, why aren't you using it? github.com/fg-labs/mako

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

Over the last few weeks I've been exploring writing a new short-read adapter trimming tool after running into frustrations with existing tools. Yesterday I made it public and pushed the first release to bioconda: github.com/fulcrumgenom...

I've seen lots of AI rewrites in bioinformatics lately, and I’m concerned because LLMs can be confidently wrong. What do the best tool builders do to make sure their rewrites are correct? How can we tell if a rewrite is flawed? I interviewed 5 scientists to find out: youtu.be/0o2XnEBDxrI

Sort your BAMs faster! I am looking for bug-resistant early alpha testers of mako to verify the speedup cl..ai..ms. I am seeing 1.1-1.9x speedups depending on data type and workload. github.com/fg-labs/mako

holodeck built with inspiration from dwgsim, which was built with inspiration from the original @lh3lh3.bsky.social wgsim. So many levels...

Catch me if you can…

Your freezer is lying to you. 🥶 We found frozen samples picked up way more artifactual C>T mutations than DNA stored at room temp. The data surprised us. 🧬👇

It's amazing to me that libdeflate has been around for ~a decade and there hasn't been a production-ready JNI wrapper for it in all that time. So this week I built jlibdeflate: github.com/fulcrumgenom...

Totally agree something has shifted. We used Claude Code extensively for fgumi and it genuinely changed our velocity on the port from Scala to Rust. The key was having deep domain expertise to guide it and catch the subtle stuff. AI as a force multiplier for experienced devs is very real now.

I'm not unique in getting here. 3 days into my effort, @robp.bsky.social wrote about using AI to rewrite piscem (combine-lab.github.io/blog/2026/02...). Then @fulcrumgenomics.com released fgumi this week (blog.fulcrumgenomics.com/p/introducin...). Something has clearly shifted in AI capabilities..

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/

If you use fgbio or UMIs at all, you should start using fgumi. Up to 100x faster, and soon 2x faster sort than samtools, it’s been a labor of love and something we’ve wanted to do for a long time.

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

Last week's fun "how quickly can I solve this" project: github.com/fulcrumgenom... - a small toolkit to i) generate more easily machine parseable kraken2 reports, and ii) filter fastqs based on kraken2 classifications.

@tfenne.bsky.social and @nilshomer.com are on the ground at #AGBT2026 this week. Big data. Tight timelines. Real decisions. #Bioinformatics is where complexity becomes something teams can actually use. If you’re here, let’s connect.

So long Scala, thanks for all the fish.

10th Anniversary Core Values blog series: Valuing People Valuing People is one of our deepest commitments: to ourselves, to our team, and to our clients. Life is messy—just like biology. When life gets complicated, we don’t look away. We step in. Read More: blog.fulcrumgenomics.com/p/core-value...

@plasmidsaurus.bsky.social next time in Boston for #ASHG25, consider catering with Bagelsaurus!

Ever want a live code review of your #bioinformatics code? DM me if you’re at #ASHG25 and I’ll take look to give you suggestions on how to improve reproducibility, maintainability, and overall engineering quality.

10th Anniversary Core Values blog series: Openness Openness is an action. It’s a positive, and proactive, choice to lean-in. It begins with a simple but powerful question: What do I know that others need to know? Read more: blog.fulcrumgenomics.com/p/core-value...

I'll be there to prove I'm not an AI. Lets meet up!

@nilshomer.com, Yossi Farjoun, and @tfenne.bsky.social will be attending #ASHG25 in Boston this year on behalf of Fulcrum Genomics. Let us know if you'll be there too!

@nilshomer.com, Yossi Farjoun and I will be attending ASHG in Boston this year on behalf of Fulcrum Genomics. Let us know if you'll be there too!

Here’s to another ten years working with awesome and talented people on challenging and impactful Bioinformatics problems! blog.fulcrumgenomics.com/p/ten-years-...

We love working with people who notice how things fit together, who make unwieldy problems work better. The 'Meet the Team' series spotlights humans behind our bioinformatics work. We hope you'll feel like you've met us — or want to. Meet Erin McAuley: blog.fulcrumgenomics.com/p/meet-erin-...

Saying no when someone offers to help deprives them of the opportunity to be generous.

What's the equivalent in #bioinformatics? xkcd.com/3113/

My Genetic Data are public: blog.fulcrumgenomics.com/p/my-genetic...

By the power of Grayskull... blog.fulcrumgenomics.com/p/create-con...

Cunningham’s Law, but making feature requests to get the correct answer. There’s got to be a German word for that.

Half the battle is knowing the right reference to use...

We try to be good #bioinformatics community members; check out our recent Open Source work @fulcrumgenomics.com blog.fulcrumgenomics.com/p/recent-ope...

git mav gist.github.com/nh13/0f32244...

"As of May 1st 2025, GATK forums will be community-driven and self-moderated. They will not be moderated or monitored by a GATK team member." See more: gatk.broadinstitute.org/hc/en-us