In Q2 Fulcrum Field Notes: @nilshomer.com on AI rewrites and minibwa, @tfenne.bsky.social on Riker for deep sequencing QC and old bioinformatics plumbing. Read the Q2 issue: resources.fulcrumgenomics.com/q2-fulcrum-f...

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

Pipeline release! nf-core/fastquorum v2.0.0 - 2.0.0! Please see the changelog: https://github.com/nf-core/fastquorum/releases/tag/2.0.0

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

@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 👇

The Scantox + LatchBio + Fulcrum webinar on the new Scantox DuplexSeq™ Mutagenesis App is now available on demand. @moonlight.bio covers Fulcrum’s approach to rebuilding and validating the bioinformatics pipeline so the infrastructure could improve without changing the science. Link below👇

Open-source bioinformatics works best when the tools are fast, inspectable, and reproducible. Our recent releases cover UMI workflows, sequencing QC, reference identification, ECS analysis, and HGVS parsing. See the one-page overview: shorturl.at/uo8iX

@nilshomer.com joined Rob Patro, @ewels.bsky.social, & others to talk AI-assisted bioinformatics rewrites on the OMGenomics show. The AI-assisted rewrite is the easy part. It is proving correctness, finding edge cases, and being around to support the tool later that’s harder. youtu.be/0o2XnEBDxrI

New release of fgbio today. Major change is to pull in HTSJDK 5 for big bumps to BAM and CRAM read/write performance, as well as full CRAM 3.1 read/write support! 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

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...

The bioinformatics community has been waiting for a modern home for the DuplexSeq method. We supported Scantox in migrating the pipeline onto Latch, validated outputs against TwinStrand's original datasets, and rebuilt the foundation so it can keep evolving with current research. shorturl.at/VmqBT

Deep QC should run on every sequencing dataset. In a new post, Fulcrum co-founder @tfenne.bsky.social explains why he built Riker, a modern successor to Picard designed to make rich sequencing QC fast enough to run every time. Blog: shorturl.at/oUTXk Repo: github.com/fulcrumgenom...

Oncology pipelines don’t stay where they were first built. They move across teams, infra, and timelines, and can start to get brittle. So we built twistcgp with @twistbioscience.com as an nf-core-based workflow for analyzing data from the Twist Oncology DNA CGP Panel. github.com/fulcrumgenom...

At #AGBTAg26, @nilshomer.com will present our work with @broadinstitute.org , @umasschan.bsky.social, and Darwin's Ark on building a comprehensive imputation reference panel for domestic cats. See the flash talk today at 4:30pm during the Plenary, or catch poster #128 during the poster sessions.

With CacheDNA we benchmarked ensilication for room‑temp DNA storage vs −80°C. Results: -100% concordance on clinical FFPE lung panel down to ~2% VAF -65% more artifactual C>T mutations at -80C than ensilication in WGS What this means for oncology, TMB, and global genomics: shorturl.at/ZqUck

We built fgbio years ago to support UMI-aware sequencing. As datasets grew, the single-threaded design started to show its limits. fgumi is the next iteration: same expected outputs, rewritten for performance and scale. github.com/fulcrumgenom... Blog post details below👇

Ever receive a BAM aligned to “GRCh38” and realize that could mean several different references? We just released ref-solver, a tool that identifies the reference genome behind BAM/CRAM/FASTA files by comparing sequence dictionaries to known builds. 🔗 whatsmygenome.fulcrumgenomics.com Read more 👇

HGVS parsing sounds straightforward until you run it at scale across real clinical variants. We just released ferro-hgvs, a Rust-based parser/normalizer that processes millions of variants per second & handles many tricky edge cases other tools struggle with. 🔗 hgvs.acgt.bio Details in blog post👇

Bioinformatics tools usually emit the final result and discard everything that led to it. That missing signal is exactly what ML models need to learn from. Fulcrum co-founder @nilshomer.com makes the case that next generation tools should be AI-ready. 🔗 blog.fulcrumgenomics.com/p/your-bioin...

Our #bioinformatics leader & VP of Ops, @moonlight.bio, will be at #PMWC26 March 4–6 in Santa Clara. PMWC continues to push the field toward turning complex biological data into real decisions. Clint will be on-site connecting with teams advancing #genomics and #PrecisionMedicine.

Open-source (nf-core–based) workflow built with @twistbioscience.com for the Twist Oncology DNA CGP Panel is now public on GitHub. Portable across local/HPC/cloud. SNVs, indels, CNVs, TMB, MSI, VEP+CIViC, QC.

@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.

One week to #AGBT2026. #Genomics data keeps growing. Pipelines keep multiplying. Turning results into something usable for research or the clinic? Still the hard part. From a #bioinformatics lens, what do you want to hear more about? Vote below

Today is International Day of Women and Girls in Science. Grateful for the women who design studies, wrangle messy data & ask the hard questions that move research forward. Your expertise makes science stronger every day. #WomenInScience

In translational/clinical work we see bioinformatics projects fail not due to science, but because early assumptions box the data in. We plan with downstream reality in mind: biology, existing data, constraints that matter. That’s how teams move fast without rework. Let’s chat & scope your project

A new *Nature Genetics* paper co-authored by Alison Meynert maps the signalling effects of every possible CTNNB1 exon 3 missense mutation. Variants in the same hotspot can differ substantially in effect. More in our blog post ↓ blog.fulcrumgenomics.com/p/why-functi...

In this final edition of our Meet the Team series, we introduce a teammate whose perspective reflects a simple premise: molecules don’t lie. After these brief interviews we hope you feel like you know each of us a little better — or want to. Meet Jess Smith: blog.fulcrumgenomics.com/p/meet-jess-...

Most teams don’t struggle with ideas, just the momentum to get there quickly. We can help. “Start with a concept, describe the desired outcome and they can build the tools to make you successful.” — Keith Brown, Founder, Jumpcode Genomics

UMI consensus isn’t hard. Making it reproducible is. Our answer to reproducibility is fastquorum, an nf-core pipeline that turns fragile, one-off UMI workflows into something boring and reliable. No hype. Just infrastructure that works. 👉 www.linkedin.com/pulse/fastqu...

New case study out: Fulcrum Genomics + Belay Diagnostics. We helped take an ECS pipeline from prototype → CAP/CLIA-ready clinical deployment, with auditability, testing to prevent regressions & cloud architecture fixes that reduced cost + avoided resource exhaustion. 👉 tinyurl.com/mtkwup9b

Most ECS pipelines focus on clean error-corrected reads. What happens after variant calling is often ad hoc. MutSeqR picks up there for mutation frequency modeling, spectrum analysis, & benchmark dose estimation across ECS platforms. More detail here: 🔗 blog.fulcrumgenomics.com/p/mutseqr-op...

Today we feature a teammate balancing rigor and delivery in complex projects. He shares views on data-driven development, disciplined iteration, and connecting lab and computational teams. We hope you’ll feel like you’ve met us — or want to. Meet Matt Stone: blog.fulcrumgenomics.com/p/meet-matt-...

Genomics is set for a big 2026: AI agents, GA4GH standards, Rust‑native workflows, long reads/ECS/SVs, and protein sequencing + AI design.

Thank you to our clients - for the challenging problems, the good questions, and the partnerships. Thank you to our team - for showing up with curiosity, rigor, and heart every single day.

ICYMI: Last week we announced MutSeqR, an open-source R package for error-corrected sequencing analysis, co-authored by our own Clint Valentine with Health Canada and U Ottawa. It brings much-needed standardization to genetic toxicology research. 🧬 🖥️ blog.fulcrumgenomics.com/p/mutseqr-op...

Proud to share that our own Clint Valentine co-authored MutSeqR, an open-source R package for analyzing error-corrected sequencing (ECS) data. Developed with Health Canada & U Ottawa, it helps bring consistency to genetic safety research. 🔗 doi.org/10.1093/bioa... #Genomics #OpenSource #MutSeqR 🧬🖥️

The whole picture: How our values connect Over the past weeks we shared our core values. If you followed this series, or worked with us as a client, collaborator, teammate, or friend, thank you. Today and every day we are thankful for you. Read more here: blog.fulcrumgenomics.com/p/10th-anniv...

At Fulcrum Genomics, Public Benefit isn’t just a principle, it's our purpose. Public Benefit has two levels, the commitment to working in biomedicine, and the daily acts of craftsmanship making the scientific ecosystem stronger. Both matter. Read more here: blog.fulcrumgenomics.com/p/core-value...

Some colleagues can to do everything and make it look effortless. This teammate reflects on balancing humility with confidence, and the power of giving your mind space to wander. By the end, you’ll feel like you’ve met us - or want to. Meet Alison Meynert: blog.fulcrumgenomics.com/p/meet-aliso...

10th Anniversary Core Values blog series: Client Focus Beyond just execution, we strive to understand the strategic context: What's the client's real need? What are the goals, constraints, and blind spots? How can we help them see around corners? Read More: blog.fulcrumgenomics.com/p/core-value...

Today we feature a teammate whose way of thinking connects games and science. It’s that mix of strategy and lightness that makes working with him such a pleasure. By the end we hope you’ll feel like you’ve met us — or want to. Meet Zach Norgaard: blog.fulcrumgenomics.com/p/meet-zach-...

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...

The best part of our work is the people who make discovery possible — thoughtful, curious, and generous with their insight. In this series we hope you’ll feel like you’ve met us — or want to. Meet Yossi Farjoun: blog.fulcrumgenomics.com/p/meet-yossi...

@nilshomer.com , @tfenne.bsky.social , and Yossi Farjoun will be in Boston for #ASHG25. If you're going to be there, let us know! #ASHG2025

10th Anniversary Core Values blog series: Excellence Excellence is a mindset and a practice. It’s not somewhere you arrive, but something you strive for, continually refining. It emerges from a culture of openness, curiosity, and accountability. Read More: blog.fulcrumgenomics.com/p/core-value...

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...

@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!

Yesterday marked ten years since Fulcrum Genomics was founded. We took a moment to reflect: blog.fulcrumgenomics.com/p/ten-years-... Thanks to everyone who’s been part of the journey.

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-...