Saw two guys stealing a bike on Bullingdon Rd yesterday and dialled 999 but couldn't get through (call failed). Dialled 999 again from Iffley Rd a minute later and connected, only to be cut off after 10s. Dangerous lack of mobile reception in East Oxford. cc @anneliesedoddsmp.bsky.social

Tip for hybrid Teams meetings: disable background noise suppression so that quiet voices aren't silenced

Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size. Demo: bede.im/deacon

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

New preprint from us @modmedmicro.bsky.social where we validate the diagnostic accuracy of a metagenomic nanopore sequencing method for respiratory RNA viruses. www.medrxiv.org/content/10.6...

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...

TLDR: don't tell an agent that it's deity theshamblog.com/an-ai-agent-...

Thanks all who listened and asked questions, and @pha4ge.bsky.social for hosting. Now on YouTube. Pro tip: don't create a 6GB file during a live demo with only 5GB free 😂

ARTIC 2 measles resources are live! As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev

Don’t miss Episode 16 of #GenomicHorizons 🧬 Join us on 12 Feb 2026 at 14:00 –15:00 UTC as @bede.im presents: “Practical panhuman host sequence depletion for responsible data sharing.” Register: us06web.zoom.us/webinar/regi... Live stream: www.youtube.com/live/FRuj2Wm... See you there!

This started as an opportunistic reuse of poppunk/sketchlib core-accessory distances, which we noticed differed between species in their shape (e.g. accessory distance at same core; faster/slower accumulation of accessory changes with core)

To do all this, we needed to reprocess all the public SARS-CoV-2 genome data in INSDC, and it became very apparent how dominated this data was by US/UK. The second half of this project became about working with teams across the world to help them get their data into INSDC.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

Kick off the first Genomic Horizons webinar of the year with @bede.im on “Practical panhuman host sequence depletion for responsible data sharing”. 📅 12 February 2026 ⏰ 14:00 – 15:00 UTC 🔗 Register here: bit.ly/4kiYW80

So anyway: BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth. Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index. github.com/RagnarGrootK... raw.githubusercontent.com/RagnarGrootK...

another look at this generational chart crime

We're Hiring! We're looking for a postdoc with bioinformatics/modelling skills to join us in an exciting microbiome ecology project in Manchester (deadline 1st March) www.jobs.manchester.ac.uk/Job/JobDetai...

The Open Visualization Academy (OVA) IS LIVE! openvisualizationacademy.org Thread follows #dataViz #infographics #dataJournalism #dataVisualization

How AI Impacts Skill Formation arxiv.org/abs/2601.20245 Studied by challenging mostly university-educated Python programmers to use async Python (Trio), so likely quite conceptually challenging. LLM users were barely faster but with a large deficit in skill acquisition. Ouch.

Harmonizing and integrating metadata across labs and systems can be difficult. In our new publication we describe an open source One Health data standard to support collaborative genomic surveillance of MPXV (Mpox virus). www.microbiologyresearch.org/content/jour... @microbiologysociety.org

By Shireen Kotay/Amy Mathers - Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance rdcu.be/e1uTu. Effects akin to gut microbiome dysbiosis/loss of colonisation resistance. To mitigate these reservoirs we need better evidence to understand what works best where.

The Somerset Levels are going under again levelslevels.uk

Nice writeup by @curiouscoding.nl on practical CI for distributing portable SIMD Rust binaries, inc to PyPI and bioconda. Includes portability lessons learned in blood with Deacon 😅 curiouscoding.nl/posts/releas...

New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...

The Cowley Low Traffic Neighbourhoods have saved 30 collisions over 3 years within the LTNs and boundary roads according to latest casualty data, analysed by @cohsat.bsky.social The Cowley LTNs were implemented in April 2021, after sporadic coronavirus lockdowns between March 2020 and March 2021.

A three act thread dear to my heart

Easy: predicting road flooding using open sensor data & measured datums (levelslevels.uk) Almost impossible: remotely ascertaining whether a given Somerset Council flood gate is open or closed, given their seldom updated website (currently 9 days since update) www.somerset.gov.uk/roads-travel...

Some bioinformatics papers: this lightweight method requires 4 gigabytes of RAM. Other bioinformatics papers: this lightweight method requires 4 terabytes of RAM.

We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬 Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions) (1/7)

This is Bam, shall I bring him in? Bites more than Sam.

Not the first paper I've been a part of, but the first one I've ever written, organized, and executed! I learned a lot getting this one done. Also, Mojo! 🔥 👇

Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...

'Can you stop an outbreak becoming a pandemic?' ARTIC Network recently delivered a workshop at the PHA4GE conference in Cape Town. Read more: www.linkedin.com/posts/artic-... @pha4ge.bsky.social

"Prolonged exposure in shared, poorly ventilated spaces… drives respiratory virus transmission more than close contact." www.nature.com/articles/s41...

We're half a decade into studies finding that improving airflow in classrooms will reduce disease transmission enormously, and that bleaching surfaces etc. does very little. And yet nothing changes. Waves of flu and colds wash over schools, and the schools pretend it's an act of God.

And if you have a .fastq.gz.mim already present, you get another up to 2x speedup (or more with >6 cores).

TIL Deacon decompresses fastq.gz 3x faster than GNU coreutils gzip/zcat. You can decompress, dehost and recompress fastq.gz using Deacon in less time than only decompressing using coreutils gzip/zcat or pigz.

github.com/bede/deacon For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️

Minimizer Density revisited: Models and Multiminimizers https://www.biorxiv.org/content/10.1101/2025.11.21.689688v1

579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm

Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2

@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2

New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions. www.biorxiv.org/content/10.1...

I want to spell this out in case the implications aren't clear: This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited. The file allowed this. Cut that - cut off all tools the public & others were using.

My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation. 4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.

I was on Last Word, the Radio 4 obituary programme, trying to sum up Jim Watson’s near-century long life.

Long term, good software requires lazy users: complain and file issues as soon as things don't work first try. If nothing else, it means documentation should be improved.

🔸️Early data suggests we could be in for a worse than normal flu season, brought on by a cluster of escape mutations in H3N2 this year that may lift the Re from 1.2 to 1.4. We are starting to see an uptick in the US. Data from BIOFIRE.

New post from me, for UK folks only, on how you need to start preparing for Apple to switch off Advanced Data Protection and the end-to-end encryption of the data you store on it. Like I said, UK only. #SunlitUplands heatherburns.tech/2025/11/10/t...