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...

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...

woke up

nobel prize. right fucking now. im serious.

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

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

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

@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...

"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...

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]

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.)

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...

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

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

Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪 #samtools #bcftools #htslib #bioinformatics

📢 HPRC Release 2 is here! Now with phased genomes from 200+ individuals, a 5x increase from Release 1. Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️: humanpangenome.org/hprc-data-re...

The magnificent seven: Oh deer! Fallow deer, Potton Wood, Beds. Small herds like this are fine and magical to behold, but like everything in nature things need to be kept in balance. We killed the wolves, hence deer stalking has its place as the man-made alternative to the wild balance.

Some of the lovely blue #wildflowers in the garden currently. #nature

Marvelling at a wonderful patch of Herb Paris (Paris quadrifolia) in a #wildlifebcn West Cambs ancient woodland. Plus my first (Midland) Hawthorn of the year in flower, and some lovely Bugle. #wildflowerhour, even though none of them are tiny plants.

Delightful Pasque Flowers on this evenings walk. A brief stop-over to Therfield Heath on the way home from work. #wildflowers #easter #nature

A beautiful morning for walking around #gamlingaywood today. Nice to see the ash stool has regained the Wood Anemone crown again. The Herb Paris patch is lookling spendid too

My first fresh looking Large White butterfly of the year, fluttering around the greenhouse until I caught it.

Going to recode the C. elegans genome to make a direworm

Public service announcement. They are not Dire Wolves. They have 20 single letter changes in their entire genomes. I’ve done shits with more mutations. Every time journalists write up a Colossus press release, They are making people stupider. Client journalism by a ridiculous company.

An early trendsetter - the English Bluebell, in Gamlingay Wood. I only saw 2 of them out of hundreds of thousands (or more). Signs of things to come. Lots of wood anemones, lesser celandines, primroses, oxlips and wild strawberries too. #wildflower #sssi #uknature

A reminder to SAMtools / HTSlib users, from the next release (probably April 2025) CRAM 3.1 will be the default version used. Use "samtools view -O cram,version=3.0" to switch back to the current 3.0. (But note 3.1 should be smaller and faster, especially on Illumina.)

Blimey. Looks like pretty much ALL of my books have been pirated by LibGen - the place that’s been scraped by generative AI developers. (thanks @gregjenner.bsky.social): www.theatlantic.com/technology/a...

This is horrible to post, but I may as well post it. We are essentially shutting down research operations in my group, which is focused on treatments for pediatric brain cancer. I’m a well funded investigator, and there’s no choice. Science can’t function without the stability of NIH

I don't know how I avoided it so long, but I'm currently weathering the storm of my first bout of Covid. Ugh! It feels every bit as uncomfortable as flu. :(

Yesterday I saw my first Brimstone butterfly of the year. It's looking good all weekend. What will I see today I wonder? Making the most of early spring before the next inevitable cold snap.

Huge win! Government announces plans to open up the Land Registry. If delivered, will finally reveal more about who owns land in England and Wales. Read my blog post for more details & how you can write to the Minister to make sure this now happens: whoownsengland.org/2025/03/06/h... 🧵1/

Stay the hell away 🤨 …

Good morning from bright blue Bedfordshire

The fact that the USA has banned visas for trans people but welcomed rapist Andrew Tate shows how all this "defending women" stuff is total bullshit

The person who should be expelled is the toadying lickspittle who did the most cursory of due diligence before proposing that the scientifically illiterate eugenics-adjacent Musk should be elected in the first place.

my thoughts on the destructive chaos targeting university research right now. Btw I've left @forbes and moved to @SubstackInc, where all my content is free: stevensalzberg.substack.com/p/the-pointl...

If you can see this, quote this sentence with a beach photo from your gallery. (East Anglia. I don't do beach crowds!)

Oops 😬