iiinova — where your digital self keeps evolving

Fulcrum Genomics @fulcrumgenomics.com · 24/09/2026

Fulcrum contributes to open-source bioinformatics by building new pipelines, improving those we maintain, and contributing to external projects. From faster alignment to transparent analysis, Public Benefit guides the work: solve real constraints and leave the field better.

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Fulcrum Genomics @fulcrumgenomics.com · 03/09/2026

Aggregate QC couldn’t answer Canal Biosciences’ question. We built a cycle-resolved framework to assess early-cycle errors, strand/base context, and ssDNA vs. dsDNA performance as the library-prep protocol evolved. See the case study: resources.fulcrumgenomics.com/hubfs/Fulcru...

resources.fulcrumgenomics.com

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Fulcrum Genomics @fulcrumgenomics.com · 24/08/2026

A good case for ensuring scientific software is safe. @science-goblin.bsky.social shares what the pixy project reinforced about building code scientists can trust, maintain, and keep extending 👇

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Fulcrum Genomics @fulcrumgenomics.com · 11/08/2026

Did you know most clinical genomics runs on research-grade code? That code has carried the field far, but benchmarking once isn't the same as verifying across versions, edge cases, & clinical use. @nilshomer.com on tool-level verification becoming routine: blog.fulcrumgenomics.com/p/benchmarki...

blog.fulcrumgenomics.com

Benchmarking is not validation

Clinical genomics runs on research-grade code. We need to validate it.

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Reposted by Fulcrum Genomics

Tim Dunn @timd.one · 22/07/2026

CRISPR off-target search can find the right locus while hiding plausible alignments within it. I wrote about how Sassy v0.2.5 uses recursive backtracking to report every reasonable alignment—more than 9× as many in under 30 seconds. blog.fulcrumgenomics.com/p/why-crispr...

blog.fulcrumgenomics.com

Why CRISPR Off-Target Search Should Report Multiple Alignments Per Locus

How Sassy enumerates every reasonable alignment without sacrificing runtime

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Reposted by Fulcrum Genomics

Alison Meynert @ameynert.bsky.social · 05/08/2026

DivRef is a resource for including common human variants and haplotypes in CRISPR off-target searches. I rebuilt the generation workflow to make its inputs, assumptions and population choices easier to inspect and change. blog.fulcrumgenomics.com/p/a-crispr-o...

blog.fulcrumgenomics.com

A CRISPR off-target search is only as good as the sequences it searches

Rebuilding DivRef so CRISPR off-target searches can account for human variation

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Fulcrum Genomics @fulcrumgenomics.com · 05/08/2026

A CRISPR off-target search cannot report a sequence it was never given. @ameynert.bsky.social explains how DivRef brings common human variants and haplotypes into the search space—and how her rebuild complements @timd.one work on Sassy. Read Alison’s post: blog.fulcrumgenomics.com/p/a-crispr-o...

blog.fulcrumgenomics.com

A CRISPR off-target search is only as good as the sequences it searches

Rebuilding DivRef so CRISPR off-target searches can account for human variation

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Fulcrum Genomics @fulcrumgenomics.com · 22/07/2026

grep is indispensable—until you need to search FASTQ files correctly. We created a hands-on guide on Sandbox.bio for searching sequencing reads and paired-end data directly in your browser 👇

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Fulcrum Genomics @fulcrumgenomics.com · 22/07/2026

Reporting one alignment per locus can commit a CRISPR off-target analysis to one scoring model too early. @timd.one explains how Sassy v0.2.5 enumerates every reasonable alignment while keeping runtime fast: >9× as many alignments in under 30 seconds. blog.fulcrumgenomics.com/p/why-crispr...

blog.fulcrumgenomics.com

Why CRISPR Off-Target Search Should Report Multiple Alignments Per Locus

How Sassy enumerates every reasonable alignment without sacrificing runtime

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Fulcrum Genomics @fulcrumgenomics.com · 01/07/2026

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...

resources.fulcrumgenomics.com

Q2 Fulcrum Field Notes

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Fulcrum Genomics @fulcrumgenomics.com · 30/06/2026

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

blog.fulcrumgenomics.com

Minibwa: alignment is never solved

Heng Li and Nils Homer revisit BWA-MEM with a faster mapper for short reads, accurate long reads, and bisulfite sequencing data.

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Reposted by Fulcrum Genomics

Heng Li @lh3lh3.bsky.social · 16/06/2026

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

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Fulcrum Genomics @fulcrumgenomics.com · 17/06/2026

@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 👇

Bioinformatics runs on a hidden layer of shared infrastructure. samtools, GATK, Picard, htsjdk, Snakemake, Nextflow, and the libraries beneath them carry a huge share of day-to-day work. Most of it stays out of sight, like city plumbing.

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Fulcrum Genomics @fulcrumgenomics.com · 09/06/2026

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👇

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Fulcrum Genomics @fulcrumgenomics.com · 28/05/2026

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

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Fulcrum Genomics @fulcrumgenomics.com · 20/05/2026

@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

youtu.be

I interviewed 5 bioinformatics experts about AI rewrites

YouTube video by OMGenomics

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Reposted by Fulcrum Genomics

Tim Fennell @tfenne.bsky.social · 20/05/2026

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...

github.com

Release 4.1.0 · fulcrumgenomics/fgbio

Summary The big news this release is primarily the update to HTSJDK 5.0.0, which brings with it to fgbio: 50-60% faster BAM writing on all platforms 30% faster BAM reading on aarch64, and modest g...

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Reposted by Fulcrum Genomics

Robert Aboukhalil @robert.bio · 14/05/2026

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

youtu.be

I interviewed 5 bioinformatics experts about AI rewrites

YouTube video by OMGenomics

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Reposted by Fulcrum Genomics

Tim Fennell @tfenne.bsky.social · 14/05/2026

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...

github.com

GitHub - fulcrumgenomics/chelae: Fast, highly accurate, read-trimming for NGS data.

Fast, highly accurate, read-trimming for NGS data. - fulcrumgenomics/chelae

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Fulcrum Genomics @fulcrumgenomics.com · 12/05/2026

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

scantox.com

Scantox Upgrades DuplexSeq™ Bioinformatics with Cloud-Based Mutagenesis App -

Scantox launches cloud based App, for its DuplexSeq™ Mutagenesis Assay kits and services. Click to learn more.

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Fulcrum Genomics @fulcrumgenomics.com · 21/04/2026

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...

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Fulcrum Genomics @fulcrumgenomics.com · 19/04/2026

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...

github.com

GitHub - fulcrumgenomics/twistcgp: Nextflow pipeline for Twist Comprehensive Genomic Profiling (CGP) panel analysis

Nextflow pipeline for Twist Comprehensive Genomic Profiling (CGP) panel analysis - fulcrumgenomics/twistcgp

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Fulcrum Genomics @fulcrumgenomics.com · 13/04/2026

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.

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Fulcrum Genomics @fulcrumgenomics.com · 08/04/2026

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

blog.fulcrumgenomics.com

Ambient DNA Preservation Without Compromising Sequencing: Our Role in Evaluating Ensilication

Whole‑genome analysis of storage-induced artifacts in tumor and normal DNA

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Fulcrum Genomics @fulcrumgenomics.com · 31/03/2026

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👇

github.com

GitHub - fulcrumgenomics/fgumi: High-performance UMI tools for NGS data analysis

High-performance UMI tools for NGS data analysis. Contribute to fulcrumgenomics/fgumi development by creating an account on GitHub.

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Fulcrum Genomics @fulcrumgenomics.com · 24/03/2026

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 👇

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Fulcrum Genomics @fulcrumgenomics.com · 20/03/2026

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👇

hgvs.acgt.bio

HGVS Normalizer - Powered by ferro-hgvs

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Fulcrum Genomics @fulcrumgenomics.com · 16/03/2026

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...

blog.fulcrumgenomics.com

Your Bioinformatics Tools Need to be AI-Ready

If you're not building tools that emit rich data for machine learning, you're wasting your compute.

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Fulcrum Genomics @fulcrumgenomics.com · 04/03/2026

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.

PMWC 2026
Precision Medicine World Conference
March 4-6, 2026
Let's talk precision medicine bioinformatics
Attending:
Clint Valentine
VP of Operations

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Fulcrum Genomics @fulcrumgenomics.com · 27/02/2026

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.

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Fulcrum Genomics @fulcrumgenomics.com · 23/02/2026

@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.

"AGBT meet your new bioinformatics team" with hand-drawn portraits of Nils Homer and Tim Fennell

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Fulcrum Genomics @fulcrumgenomics.com · 17/02/2026

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

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Fulcrum Genomics @fulcrumgenomics.com · 11/02/2026

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

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Fulcrum Genomics @fulcrumgenomics.com · 09/02/2026

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

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Fulcrum Genomics @fulcrumgenomics.com · 05/02/2026

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...

blog.fulcrumgenomics.com

Why Functional Resolution Matters for Interpreting CTNNB1 Cancer Mutations

At Fulcrum, we’re often brought into projects where variants have already been called, annotated, and grouped.

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Fulcrum Genomics @fulcrumgenomics.com · 04/02/2026

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-...

blog.fulcrumgenomics.com

Meet Jess Smith

Molecules Don’t Lie — If You Know How to Ask

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Fulcrum Genomics @fulcrumgenomics.com · 28/01/2026

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

Text on a blue background reading "They helped us move faster than we could on our own."
Keith Brown, Founder, Jumpcode Genomics

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Fulcrum Genomics @fulcrumgenomics.com · 26/01/2026

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...

linkedin.com

fastquorum: Making UMI consensus boring (in the best way)

If you’ve worked with UMI-tagged sequencing data long enough, you already know the theory. Tag molecules early, group reads that came from the same original fragment, collapse them into a consensus, a...

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Fulcrum Genomics @fulcrumgenomics.com · 20/01/2026

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

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Fulcrum Genomics @fulcrumgenomics.com · 15/01/2026

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...

Schematic of a genomics pipeline with MutSeqR

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Fulcrum Genomics @fulcrumgenomics.com · 09/01/2026

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-...

blog.fulcrumgenomics.com

Meet Matt Stone

Head of Single-Cell and Spatial Sequencing

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Fulcrum Genomics @fulcrumgenomics.com · 30/12/2025

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

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Fulcrum Genomics @fulcrumgenomics.com · 19/12/2025

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.

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Fulcrum Genomics @fulcrumgenomics.com · 10/12/2025

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...

blog.fulcrumgenomics.com

MutSeqR: Open Standards for Error-Corrected Sequencing Analysis

Standardizing Error-Corrected Sequencing Data Analysis

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Fulcrum Genomics @fulcrumgenomics.com · 03/12/2025

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 🧬🖥️

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Fulcrum Genomics @fulcrumgenomics.com · 27/11/2025

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...

blog.fulcrumgenomics.com

10th Anniversary Core Values: The Intersection

How our values connect and guide us forward

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Fulcrum Genomics @fulcrumgenomics.com · 19/11/2025

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...

blog.fulcrumgenomics.com

Core Value: Public Benefit

Fulcrum Genomics 10th Anniversary Series

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Fulcrum Genomics @fulcrumgenomics.com · 12/11/2025

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...

blog.fulcrumgenomics.com

Meet Alison Meynert

Between the Lines of Code and Conversation

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Fulcrum Genomics @fulcrumgenomics.com · 06/11/2025

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...

blog.fulcrumgenomics.com

Core Value: Client Focus

Fulcrum Genomics 10th Anniversary Series

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