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

fgbio in use again! Who says we can't have OSS #bioinformatics from an commercial organization? www.nature.com/articles/s41...

Python is a simple language, but using it isn't always easy. Today I reflected on the following code. To really understand it, one must learn: generators, type hinting, pytest fixtures, advanced usage of fixtures, monkey patching the OS environment, mocking impure environments, generators...

How to use Conda without running afoul of Anaconda licensing. Read more on our blog: #bioinformatics #conda #software open.substack.com/pub/fulcrumg...

New release of fastquorum! This nf-core #nextflow fgbio Best Practices FASTQ to Consensus Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs).

Breaking: from the Series-A MVP slide deck!

Public service announcement. They are not Dire Wolves. They have 20 single letter changes in their entire genomes. I’ve done shits with more mutations. Every time journalists write up a Colossus press release, They are making people stupider. Client journalism by a ridiculous company.

Please just use grayskull for (bio)conda recipes as a starting point...

Crappy shell scripts wrapped in a Nextflow process are still crappy...

UI in #bioinformatics is just making the command line prettier...

He was just part of my life, time to let him go… goodbye iceman.

#bioconda #bioinformatics

Everything will be forgiven if you just wrap it in Nextflow...

"spectacularly slow" also applies to me right now...

fqgrep release 1.1.0 now speeds up searching FASTQ files! Thank-you to both Markus Schlegel from @activegroupgmbh.bsky.social for updating seq_io and Nicholas D. Crosbie of grepq for some competition and inspiration. See more: github.com/fulcrumgenom...

If I have to go diving through your code to work out how the API works, your docs have failed.

I just wanted to know where I messed up my YAML file and now I am maintaining a new package. github.com/nh13/ruamel_...

Reminder for the rest of you heathen time changers...

I didn't know off-targets effects could result in a Mouse when we wanted a Mammoth...

If you’re in Boston 🌆 and use #nf-core or #Nextflow, join our regional channel! 🌐 We’re starting monthly meetings 📅 to foster community growth and mutual support! 🤝 nfcore.slack.com/archives/C08...

My top-THREE non-Roche-SBX #AGBT25 takeaways: 1. Spatial Genomics is the new shiny object 2. Methylation detection was ubiquitous and varied 3. Normalization of libraries improved but was iterative If you're looking for Bioinformatics help, give me a call!

So many DNA-methylated assays at #AGBT25. Wait until they hear about methylated RNA. #bioinformatics