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...

As expected, unfortunately. If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further. Time to move on to more trusted and transparent solutions.

Our method for genome size estimation from long-read overlaps is now published 🥳 academic.oup.com/bioinformati...

“my brain is open” users.monash.edu/~normd/docum...

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

RIFs at CDC. Destroying the Epidemic Intelligence Service, NCIRD, NCIPC & a dozen other areas/divisions/branches will cause enormous harm and suffering to America, and indeed to the whole world. Call your Reps about it. Then call them again.

Our recent paper on rifampicin resistant subpopulations in M. tuberculosis (M. tb) has been published at JAC-antimicrobial resistance. I am really happy to see this work published just hours before submitting my DPhil thesis! 🔗👇 doi.org/10.1093/jaca...

For more information about the Friday night massacre at CDC, I wrote up an analysis of who got terminated and what that means for public health. Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble. rasmussenretorts.substack.com/p/the-death-...

So what's the equivalent of `perf record && perf report` on a MacBook? I want to see the generated assembly and which lines are hot.

Last week we were in the Washington Post for our characterization of Robertsonian chromosomes. This week we are entering our 10th day of being shut down and all of our research is on hold. To help me feel not-so-bad, here is a thread of some studies we released right before the shutdown 🧵 [1/n]...

Funny story, though, we found this gene in NCBI databases, but it was annotated in Streptococcus pneumoniae! This is surely human contamination in a bacterial strep sample that was not properly filtered. Lesson: use CHM13, or better yet a pangenome, when filtering for human contamination...

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

Deacon 0.11.0: - Local server mode - Ultra-careful handling of non-ACGT - Faster indexing & index loading - Denser index now stores k-mers not hashes - xxHash & FxHash replaced with rapidhash::fast - Bug fixes Thanks @curiouscoding.nl (and others!) for contributions github.com/bede/deacon/...

"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...

Looking for people to test the latest version of simd-sketch. It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower). 'cargo install simd-sketch' is right there under your fingertips ;) github.com/RagnarGrootK...

FxHashSet::<u32>::contains throughput is wild! - Up to 4x slowdown for negative queries due to probing. - Positive queries are fast for small tables, but slow in RAM because they need 2 cache misses. Lots of variance depending on the load factor, ie whether n is close to 87.5% of a power of 2.

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1... Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

Terrific new feature presented by @theo.io on @pathoplexus.org called SeqSets for generating DOIs for sequence subsets used in publications, that can then be tracked for impact via CrossRef that will allow data generators to track impact! #IMMEMXiV

Front page of Hacker News 🫨 bsky.app/profile/bede...

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...

First rate BBC journalism that somehow didn't make the cut for #r4today www.bbc.co.uk/news/article... @andyverity.bsky.social

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Zstandard's --long range mode works wonders for assemblies, but needs uninterrupted single line sequences. *AllTheBacteria 661k, multiline fasta* gzip (pigz): 751GB zstandard --long: 641GB (30% original size) *Single line fasta* gzip (pigz): 700GB zstandard --long: 232GB (10% original size)

"The Agriculture Department will not require poultry companies to limit salmonella bacteria in their products, halting a Biden Administration effort to prevent food poisoning from contaminated meat." www.seattletimes.com/business/usd...

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

Claude's kryptonite: incredibly mundane biology questions

🎉 New in August: Measles virus joins Pathoplexus! Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV pathoplexus.org/measles/search 5/10

Paraseq 0.4 is out now! With double the throughput for processing paired-end input :) github.com/noamteyssier...

Latest by us! An mRNA-based broad-spectrum antiviral inspired by ISG15 deficiency protects against viral infections in vitro and in vivo | Science Translational Medicine www.science.org/doi/10.1126/...

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples

Deacon 0.9.0 can filter FASTA at well over 2Gbp/s on an AMD CPU from 2021. Compression is very limiting, but I suspect ~1Gbp/s is possible for fastq.gz with a modern CPU. Thanks @curiouscoding.nl for a monumental perf PR! Release 0.9.0 github.com/bede/deacon/... www.biorxiv.org/content/10.1...

taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!

Ever had to pause genomic surveillance due to enzyme shortages?🫣 Happy to share our new preprint with the solution inside 🦹‍♀️💪 biorxiv.org/content/10.110… @scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com

Interested in respiratory metagenomics? We assembled nearly all of the virus genomes in a respiratory verification panel manufactured by ZeptoMetrix. Blog: artic.network/2025-07-26_p... Assemblies: github.com/bede/zmrp @scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social

📣 Deacon 0.8.0 available on Bioconda - Much faster search and depletion through improved work distribution on multicore systems. My fastq.gz benchmark now runs at 400Mbp/s on Apple M1. - Dual default match thresholds for greater accuracy Details: github.com/bede/deacon/... 1k downloads! 🐥

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3

Little writeup on the speed of fasta parsers, at last. Basically: both needletail and paraseq are process input linearly, and thus have a limit around 4 GB/s. By giving each thread its own slice of the input file, we're limited by RAM bandwidth instead :) curiouscoding.nl/posts/fasta-...

Reducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab Freezer https://www.biorxiv.org/content/10.1101/2025.06.11.658579v1

Textbook case of A-pillar blindness

📢New job posting!📢 Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬 My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on! 1/5

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...

tl;dr: Royal Society: "I say, old chap, we're in a bit of a hole with your FRS. Do you think you could help us out and do the decent thing?" Musk: "HAHAHAHAHA Go fuck yourselves"