iiinova — where your digital self keeps evolving

Tim Fennell @tfenne.bsky.social · 28/09/2026

I'm winding up to generate a mostly large joint callset (about 10k samples) through GATK's HaplotypeCaller to make gVCFs, and then on into GenomicsDB. I'm curious - are folks still actively using HaplotypeCaller / GATK for germline joint genotyping? Or are folks moving on to something else?

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Tim Fennell @tfenne.bsky.social · 28/09/2026

New release of chelae over the weekend. The fastest adapter and qual trimming software you've probably never heard of 😉 Still measures the fastest of the bunch, though AdapterRemoval v3 isn't too far behind. Now with support for streaming interleaved FASTQ! 🧬 🖥️ 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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Tim Fennell @tfenne.bsky.social · 24/09/2026

Do you use kraken2? If so, don't skip the new release yesterday, now available on bioconda: github.com/DerrickWood/... Includes a PR from me that speeds up both database load (up to 3X) and classification (24-39% improvement)!

github.com

Release v2.17.2 · DerrickWood/kraken2

Minor release to fix bugs with k2 wrapper, speeds up merging using multi-threading. We have another release pending that will see significant speed ups to classification. What's Changed Multi-data...

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Nils Homer @nilshomer.com · 14/09/2026

bwa-mem3 v0.12.0 is out 🧬 Since v0.10.0: faster on both Arm & x86 (--fast is now ~2× minibwa and stock is within ~15% on x86) while staying a byte-identical (--compat). It also brings ~30–40% faster methylation and a big memory-safety pass. github.com/fg-labs/bwa-... #bioinformatics #genomics

github.com

Release v0.12.0 · fg-labs/bwa-mem3

0.12.0 — faster on both architectures, a faster --meth, and a large safety pass A broad optimization release that speeds up both Arm and x86 (unlike 0.11.0, which concentrated on Arm), plus a methy...

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Ashland Poetry Press @ashlandpoetrypress.bsky.social · 01/09/2026

@ktlandon.bsky.social 's debut collection, Abide, launches today! 2025 Richard Snyder Prize Winner, selected by @kimaddonizio.bsky.social Abide is available at @bookmobile-itasca.bsky.social , Amazon, & elsewhere now! #bookrelease #poetry #poetrycommunity #newbook #itasca #buyabook #poems

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Jess Smith @nanojess.io · 31/08/2026

Every time I read a paper like this I just think about what a PITA it's going to be to design off-target NGS assays that are suitable for regulatory review.

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Tim Fennell @tfenne.bsky.social · 26/08/2026

dupblaster 0.3.0 is released! The new release adds: - optional tmp file compression with zstd - sequencing (optical) vs. library duplicate detection - incremental performance improvements On top of existing: - fastest and most accurate query-grouped duplicate marking - comprehensive QC stats 🧬🖥️

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Nils Homer @nilshomer.com · 25/08/2026

fgumi v0.7.0 is released: github.com/fulcrumgenom... 1. sort is 28% faster; 2-3x faster than samtools 2. improved CODEC consensus calling 3. dedup now outputs metrics closer to picard MarkDuplicates and dupblaster 4. retag is a new tool that can copy/move/delete SAM tags

github.com

Release v0.7.0 · fulcrumgenomics/fgumi

For those running the fgumi command line tools v0.7.0 makes sort faster, hardens CODEC consensus, and brings dedup metrics to Picard/dupblaster parity. Sort is up to 28% faster — and 2–3× faster th...

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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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Tim Fennell @tfenne.bsky.social · 24/08/2026

Did whoever coined "dovetailed" as the term for an NGS read-pair where the 3' ends extend past their mate's 5'-ends have *any* knowledge of woodworking? In a field of terrible names, this one wins for me because it invokes the exact opposite the originators' intent/usage.

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Tim Fennell @tfenne.bsky.social · 05/08/2026

Awesome forensics work by @ameynert.bsky.social to figure out all the issues and build a more robust pipeline and more complete and accurate DivRef!

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Tim Fennell @tfenne.bsky.social · 01/08/2026

Maybe three weeks ago, I* refactored some code out of dupblaster and methylsieve for using dedicated threads with large buffers for read-ahead and write-behind. Why? Because it turns out, even in Rust, it's still hard to write threading code that "just works". github.com/tfenne/rawb-io

github.com

GitHub - tfenne/rawb-io: Read-ahead / write-behind byte IO: threaded Reader/Writer that decouple a pipeline stage from the kernel pipe via a background thread and a byte ring buffer

Read-ahead / write-behind byte IO: threaded Reader/Writer that decouple a pipeline stage from the kernel pipe via a background thread and a byte ring buffer - tfenne/rawb-io

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Nils Homer @nilshomer.com · 23/07/2026

bwa-mem3 v0.7.0 is out. 5–24% faster than v0.6.0, output byte-identical; upgrade and it's free. If you do methylation: reworked bisulfite path with TAPS support too. github.com/fg-labs/bwa-mem3/releases/tag/v0.7.0

github.com

Release v0.7.0 · fg-labs/bwa-mem3

0.7.0 — methylation accuracy, a sharper --fast, and broad speedups This is primarily a methylation release. The bisulfite path was reworked to a chemistry-aware contract — TAPS support, a NEUTRAL -...

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Nils Homer @nilshomer.com · 14/07/2026

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

github.com

GitHub - fg-labs/unum: Fulcrum-owned Rust HLA/KIR genotyper (strangler port of T1K)

Fulcrum-owned Rust HLA/KIR genotyper (strangler port of T1K) - fg-labs/unum

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yaoi gagarin @mel.bzky.team · 12/07/2026

well okay so the english won against the norwegians but in only a few days theyll have to face the french. anyway thats quite enough about September 25th 1066, lets look at some football news

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Andrew Whitwham @whitwham.bsky.social · 09/07/2026

Release 1.24 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪🧬🖥️

htslib.org

Samtools

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Nils Homer @nilshomer.com · 09/07/2026

🚀 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...

github.com

Release v0.7.0 · fulcrumgenomics/ferro-hgvs

Added (reference) validate manifest schema/version at load, fail loud on an incompatible reference (#1003) (mosaic) parse predicted-wrapper and whole-entity-LHS =/ forms (#992) (protein) parse ins...

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Tim Fennell @tfenne.bsky.social · 09/07/2026

More fun with fable yesterday. A coworker thought they'd cracked the code by asking opus to pose questions to a fable sub-agent in Claude Code. Dear reader, they had not.

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Randall Munroe @xkcd.com · 08/07/2026

Offside xkcd.com/3268/

Comic. [chessboard with red dotted line and flag at second line. Highlighted rook is positioned next to King behind the red line.] [caption] I thought I had checkmate, but I didn’t realize my rook was offside.

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Rob Patro @robp.bsky.social · 07/07/2026

My journey with @anthropic.com's Fable 5 model has been a very short one; characterized by "No". So, in my most recent blog post, I explain why I think "Fable is not a useful model" combine-lab.github.io/blog/2026/07...

combine-lab.github.io

COMBINE-lab - Fable is not a useful model

COMBINE-lab develops algorithms, data structures, and software for high-throughput genomics.

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Tim Fennell @tfenne.bsky.social · 06/07/2026

In other news I released a tool called methylsieve ~3 weeks ago, thinking it would just be a better "filter unconverted reads" tool that'd slot in between alignment and sorting. Then I got frustrated that most tooling does m-bias filtering wrong ... now I have a version 0.2 coming soon... 🧬 🖥️ 🧵

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Tim Fennell @tfenne.bsky.social · 06/07/2026

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"

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Tim Fennell @tfenne.bsky.social · 06/07/2026

Our blog traffic isn't high enough to get this awesome image by our graphic designer the views it deserves:

My hobby: burning massive amounts of compute on AI coding ... to save the genomics community even more compute.

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Nils Homer @nilshomer.com · 04/07/2026

🚀 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-...

github.com

Release v0.5.0 · fg-labs/bwa-mem3

0.5.0 (2026-07-04) Features add opt-in --seed-order seed reordering (default off, byte-identical) (#186) (04749a1) add opt-in --smem-dedup (dedup identical SMEMs before chaining) (#187) (1384972) ...

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Andrew Carroll @acarroll.bsky.social · 01/07/2026

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

andrewcarroll.github.io

The Best of Both Worlds - Assessing MiniBWA

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

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Tim Fennell @tfenne.bsky.social · 02/07/2026

I was really hoping that in the time it's been away, @anthropic.com might have made the biology related guardrails in fable better. But no. Me: Are you able to do anything biology related yet, or are your guardrails still ludicrously coarse? Claude: Switched to Opus 4.8

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Tim Fennell @tfenne.bsky.social · 30/06/2026

So many things getting faster recently!

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Tim Fennell @tfenne.bsky.social · 28/06/2026

@psy-fer.bsky.social I've been trying out rustar after struggling to get STAR to run on mac. It's great - thank you!! Have you spent much time optimizing speed/performance? I'd be happy to try and help if contributions are welcome and you think there's opportunity for improvement.

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Tim Fennell @tfenne.bsky.social · 22/06/2026

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...

github.com

GitHub - fulcrumgenomics/dupblaster: Blazingly fast, streaming duplicate detection for NGS data

Blazingly fast, streaming duplicate detection for NGS data - fulcrumgenomics/dupblaster

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Tim Fennell @tfenne.bsky.social · 17/06/2026

Top of the list of things I wouldn't have done without Claude/AI this week: write a harness that runs tens of thousands of iterations of fastp to find 4 deadlock bugs (really 1, repeated in four places) that cause fastp to infrequently hang at the end of processing. And of course fix, and PR it.

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K. T. Landon @ktlandon.bsky.social · 16/06/2026

My debut collection, ABIDE, is now available for pre-order and has this dream of a cover with artwork by Jill Schwaiko and design by Nick Fedorchak of @ashlandpoetrypress.bsky.social. I get a little teary every time I look at it – can’t believe it’s real!

Cover for the K. T. Landon's poetry collection, titled ABIDE. Features a painting of two yellow big-horn sheep flanked by red canyon walls gazing up at a yellow moon.

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Tim Fennell @tfenne.bsky.social · 14/06/2026

How are folks in the US watching the World Cup this year? I’m trying YouTube TV and so far I hate it. Is anything else better?

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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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Heng Li @lh3lh3.bsky.social · 30/05/2026

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

biorxiv.org

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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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Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/05/2026

Turns out I presented Sassy yesterday without realising it has been published! Finally officially a coauthor with @rickbitloo.bsky.social 😆 doi.org/10.1093/bioi...

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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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Tim Fennell @tfenne.bsky.social · 15/05/2026

I'm very excited - three of my current favorite authors have new books out in the last ~10 days! @annleckie.com's Radiant Star in the Radch universe @marthawells.com's Platform Decay (Murderbot) @mattdinniman.bsky.social's A Parade of Horribles All of them from series that are well worth reading!

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Andrew Liptak @andrewliptak.com · 14/05/2026

@annleckie.com's latest novel, Radiant Star, is now out in bookstores. It was a useful excuse to finish an interview I'd conducted with her for the 10th anniversary of Ancillary Justice, in which we talked about the book, Rome, finding the personal stories in galactic empires and more:

andrewliptak.com

Ancillary Interview

Ann Leckie on Ancillary Justice, finding the personal stories in galactic empires, and what she's learned about writing

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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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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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Tim Fennell @tfenne.bsky.social · 01/05/2026

Finally pushed out a 5.0.0 release of HTSJDK. Headlines: - CRAM 3.1 write support (finally!) - Much faster CRAM reading (46%) and writing (20-43%) - Much faster BAM reading (6-31%) and writing (51-58%)

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Tim Fennell @tfenne.bsky.social · 22/04/2026

It's turtles all the way down!

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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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Heng Li @lh3lh3.bsky.social · 17/04/2026

The correct link: lh3.github.io/2026/04/17/t...

lh3.github.io

The AI Rewrite Dilemma

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