Bede Constantinides

Remarkably swift response from @anneliesedoddsmp.bsky.social and team – thank you

Interesting, this was a few hours before that apparently caught fire. Given that EE isn't usable in half of the streets between Cowley and Iffley, I'm not too surprised that the 999 coverage is also poor.

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

Silver lining: a helpful constraint on MacOS memory usage for a few years?

Feedback welcome, the chunked parsing isn't pretty.

Yes, see wasm branch github.com/bede/deacon

Thanks for sorting that :-) What's the main thing missing from wasm simd128 for this application?

Thanks! On paper it should be straightforward for pure Rust crates that don't do POSIXy things like thread management. Once simd-minimizers was patched, the main challenge here was (large) file IO at the wasm boundary. Also, wasm64 for Rust isn't viable yet, meaning a small address space for now.

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

Typo? But yes for sure

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).

Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study Background Clinical metagenomics (CMg) offers high-throughput respiratory pathogen detection with a wider range than targeted, probe-dependent diagnostics. Sequencing cost and the challenges of high h...

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...

This looks fun 👨‍🍳

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 😂

A webpage section listing three resources related to measles virus genomic epidemiology. The first item shows an icon and the heading ‘Measles virus genomic epidemiology’ with a subheading ‘A primer on measles virus genomic epidemiology and why we do it.’ The second item shows an icon and the heading ‘artic-measles/400/v1.0.0 Primer Scheme’ with a description of the ARTIC-network primer scheme for sequencing measles virus. The third item shows an icon and the heading ‘ARTIC-network MEV wet-lab protocol’ with a description of the wet-lab protocol for sequencing MEV using the artic-measles/400/v1.0.0 primer scheme.

A webpage section titled ‘User‑interface pipelines using Epi2me,’ displaying four items. The first item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME’ and describes using EPI2ME to run the ARTIC amplicon‑nf pipeline without the command line. The second item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Illumina Data,’ again describing use of EPI2ME to run the amplicon‑nf pipeline without the command line. The third item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Oxford Nanopore Data,’ with the same description. The fourth item shows an icon with the heading ‘amplicon‑nf: Viewing outputs of the pipeline in EPI2ME,’ describing how to view outputs of the amplicon‑nf pipeline within EPI2ME.

A webpage section titled ‘Command line interface pipeline SOPs.’ The first item shows an icon with the heading ‘Fieldbioinformatics: viral amplicon sequencing bioinformatics SOP’ and labels indicating ‘Nanopore | bioinformatics.’ A second section titled ‘Phylogenetics and Interpretation’ includes an icon with the heading ‘MeV Phylogenetics’ and a description stating it contains resources and protocols for measles virus alignment and phylogenetics.

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!

Core trees, core-accessory distance plots, and model fits for four bacterial species (A) Mycobacterium tuberculosis, (B) Streptococcus pneumoniae, (C) Escherichia coli and (D) Listeria monocytogenes.)

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.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

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...

This. And the inevitable oled burn-in.

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...

U.S. and global steel production over the past decade. The highlighted year-over-year increase in U.S. output is real but small, and looks very different when shown in context versus a tightly cropped comparison.

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...

Screenshot of the OVA website, showing all courses

The Open Visualization Academy (OVA) IS LIVE!
openvisualizationacademy.org

Thread follows #dataViz #infographics #dataJournalism #dataVisualization

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