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 - 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

github.com

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

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 - 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

github.com

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

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

🚀 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...

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...

github.com

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.

Offside xkcd.com/3268/

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 - Fable is not a useful model

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

combine-lab.github.io

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... 🧬 🖥️ 🧵

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"

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

🚀 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-...

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) ...

github.com

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...

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

So many things getting faster recently!

Fulcrum Genomics@fulcrumgenomics.com · last mo.

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

@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.

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

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

github.com

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

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.

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!

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?

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👇

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...

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

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...

@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

I interviewed 5 bioinformatics experts about AI rewrites

YouTube video by OMGenomics

youtu.be

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'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!

@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:

Ancillary Interview

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

andrewliptak.com