Note with the new release (1.24) of samtools / bcftools / htslib, we took the decision to drop CRAM 4.0 support. This is because htslib was the only thing that implemented it AFAIK, it was an experimental prerelease and not an adopted standard, and sadly it wasn't as well engineered as it should be

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

🚀 new bwa-mem3 is out. Why use it? - 🏛️keep using a bwa-mem variant (avoid revalidation/reprocessing) - 🚅 1.7x faster/20% less memory than bwa-mem2 - 🧬native methylation support (asymmetric scoring) - ✅ matches bwa-mem2 output - 👊opt-in knobs to go even 2x faster bwa-mem3.readthedocs.io/en/latest/

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

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%)

jonny over on masto doing god's work: > anthropic [is running] an ENTIRE AD CAMPAIGN around "Claude code is written with claude code" and after the source was leaked that has got to be the funniest self-own in the history of advertising because OH BOY IT SHOWS. neuromatch.social/@jonny/11632...

jonny (good kind) (@jonny@neuromatch.social)

Attached: 1 image reminder that anthropic ran (and is still running) an ENTIRE AD CAMPAIGN around "Claude code is written with claude code" and after the source was leaked that has got to be the funn...

neuromatch.social

On Friday we revealed the Companies House vulnerability letting anyone access the private dashboard of any UK company. This is the moment I first saw it demonstrated. My reaction says it all. What do we know? What don't we know? What should companies do now?

At last! All remaining hereditary peers in the UK House of Lords will go in May 92 men, mostly old, will no longer have a significant voice in our governance simply due to *who their parents were*, usually based on a forgotten deed by a long, long dead ancestor www.bbc.co.uk/news/article...

Hereditary peers to be removed from Lords as bill passes

The bill abolishes the 92 seats reserved for peers who inherit their titles through their families.

bbc.co.uk

woke up

nobel prize. right fucking now. im serious.

⚖️🌎 BIG NEWS THIS WEEK 🌍⚖️ https://goodlaw.social/kxzk

Climate crisis: We’ve filed our challenge to Starmer’s delay | Good Law Project

Global heating is all around us and the government isn’t doing enough – so we’re taking them to court

goodlaw.social

I am delighted to announce the release of my latest project: Fully documented source code for The Sentinel, Geoff Crammond’s 1986 masterpiece. Here’s the repository; deep dives coming soon. See thread for details. 1/9 github.com/markmoxon/th... #retrocomputing #retrogaming #bbcmicro #c64 #8bit

GitHub - markmoxon/the-sentinel-source-code-bbc-micro: Fully documented and annotated source code for The Sentinel on the BBC Micro

Fully documented and annotated source code for The Sentinel on the BBC Micro - markmoxon/the-sentinel-source-code-bbc-micro

github.com

How about we get rid of political donors all together? Ban the wealthy elite from owning UK politicians.

UK ministers urged to cap political donations to ‘rebuild voter confidence’

Letter from 19 organisations says a cap would help to protect democracy, weeks after £9m donation to Reform UK

theguardian.com

@funranium.bsky.social Always be stealing Dune memes!

SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.

The usual process ofbuilding modern C++ packages from GitHub... Step 1: download and build yet another new version of cmake. Bah Humbug. (I tried edited it and no, it did indeed need some new feature. Sigh) I miss the old ways.

A lovely collection of fungi from WildlifeTrustBCN's Gamlingay Woods. #fungi

Never forget: At breakneck speed we are leaving the stable Holocene climate in which human society developed and thrived. Weather extremes are outside historical experience. Sea-level rise is accelerating. Dangerous tipping points are ahead. Graph: ed-hawkins.github.io/climate-visu...

It's curious to see grokipedia is up and has samtools, SAM and BAM pages all with a flurry of edits. Oddly, most of those edits are correcting minor edits in the Wikipedia pages it based its content on (presumably via some AI rewriting tool). A shame the originals weren't edited too.

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

Efficient and accurate search in petabase-scale sequence repositories - Nature

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

nature.com

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary." engineering.fb.com/2025/10/06/d...

Introducing OpenZL: An Open Source Format-Aware Compression Framework

OpenZL is a new open source data compression framework that offers lossless compression for structured data. OpenZL is designed to offer the performance of a format-specific compressor with the eas…

engineering.fb.com

Bede Constantinides@bede.im · 11mo ago

Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

biorxiv.org

Note: OLD POST! (2023), but I just noticed it. While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools? Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)

Casey Bergman@caseybergman.bsky.social · 3y ago

Important comparison of Bcftools and GTK in simulated Drosophila genomes: "by benchmark analyses with a simulated insect population...Bcftools mpileup performs better than GATK HaplotypeCaller in terms of recovery rate and accuracy regardless of mapping software."

I'm sorry, worldwide, irrevocable, non-exclusive, transferable permission to my voice and likeness? For what now? In any manner for any purpose??? This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.

minimap2.com is potentially a phishing site. Please don't use anything from that website. github.com/lh3/minimap2...

Phishing site : minimap2.com · Issue #1316 · lh3/minimap2

Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...

github.com

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

Nigel Farage looks uncomfortable as Jamie Raskin uses his opening statement to absolutely demolish him

Preprint alert! We present K2Rmini, an ultra-fast, grep-like tool that extracts sequences of interest from FASTA/FASTQ files based on their k-mer content. www.biorxiv.org/content/10.1... A thread

Accelerating k-mer-based sequence filtering

The exponential growth of global sequencing data repositories presents both analytical challenges and opportunities. While k - mer-based indexing has improved scalability over traditional alignment fo...

biorxiv.org

Are juvenile common lizards normally black, or is this a melanistic one? It was tiny. Seen at #RSPB #Fowlmere.