Nick Sanderson

Oxford congestion charge partially suspended after ring road shuts The decision is made after Oxford's ring road was shut due to a fire.

Telephone mast on fire possibly the reason?

www.bbc.co.uk/news/article...

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

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...

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...

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...

1/4 Thrilled to get this metagenomic diagnostic study over the line. We have an in house method that targets RNA viruses in respiratory samples, and evaluated this against 344 prospective samples tested by multiplex PCR.

www.medrxiv.org/content/10.6...

Oh this is fun

Are you a post-doctoral microbiologist interested in characterising bacterial resistance evolution and want to apply your knowledge and expertise to developing new therapeutics for Klebsiella (and other Enterobacterales) infections? Then we need you! Apply now bit.ly/3MX39Ce close date March 13th 👀

International Day of Women and Girls in Science 👩‍🔬

Proud to work alongside the scientists in our #microbiology lab whose work in antimicrobial resistance, public health and diagnostics has real-world impact!

#WomenInScience #AMR #PublicHealth @medsci.ox.ac.uk @ox.ac.uk @oxfordbrc.bsky.social

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)

Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...

Clarion news: We’re leaving Twitter (’X’). We can’t condone the objectionable content it now promotes, which goes against everything we believe and the Clarion tradition. Our live posting is now here on Bluesky, with all this plus much more in our email newsletter twice a week.

I do enjoy the out-of-office to editorial-manager auto-reply ping pong of holiday review requests

Good luck to the journal editor trying to get me to review a paper today with a 14 day turnaround 🙃

CRICKET

a man is talking on a phone and saying hello it have you tried turning it off and on again ALT: a man is talking on a phone and saying hello it have you tried turning it off and on again

www.zotero.org/support/kb/d...

It's 2025, why are all reference managers still crap.

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon

Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1

Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv

@bedec.bsky.social presenting his deacon human filtering tool poster pitch at #ABPHM25

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection | Journal of Clinical Microbiology Diagnosis of orthopedic device-related infection is challenging, and causative pathogens may be difficult to culture. Metagenomic sequencing can diagnose infections without culture, but attempts to de...

Thanks, but we’re very family with saponin (see paper we published in 2022). This paper was specifically looking at adaptive sampling as another means of host depletion. As saponin can’t always be used

journals.asm.org/doi/full/10....

Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue Metagenomic approaches to diagnosis of prosthetic joint infections promise more accurate and more rapid diagnosis. However, the high host DNA to bacterial DNA ratio is a challenge. Nanopore adaptive s...

A new preprint from us. Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue. Where high host contamination is still a big issue. We find modest improvements in bacterial yield. But not enough to improve diagnostics

www.medrxiv.org/content/10.1...

Can’t believe this didn’t go viral.
All the best, Nick

Roses are red,
Violets are blue,
Your grant will be funded,
As long as it's bird flu

Been near any chickens recently?

Come and work with us!

We are looking for a Medical Statistican.

Closing date: 4 Feb 2025

bit.ly/3E5JtaI

Come and work with us!

Programme Manager is a key central role that sets large strategic objectives and manages practical issues across the MMM Unit.

Grade 9, £55,636 - £64,228, deadline noon 6 Jan 25

bit.ly/4fGgnwv

I've had requests for the raw squiggle data for this paper. I know a number of groups found that useful from our first R10 evaluation paper. So our raw fast5 (sorry not pod5) files for R10.4.1 are on ENA:
ERR13848445 E .coli
ERR13848444 P. aeruginosa
ERR13848443 S. aureus
ERR13848442 K. pneumoniae

That’s it, now @nedboulting.bsky.social and @iandunt.bsky.social are here, I no longer need to look at X/twitter. This place is getting really good

pQEB1: a hospital outbreak plasmid lineage carrying bla KPC-2 While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPE) from patient colonisation and clinical infections at Birmingham’s Queen Elizabeth Hospital (QE), we identified...

Our latest paper now published in MGen. Long read surveillance identifying inter-species spread of a KPC plasmid in Birmingham

www.microbiologyresearch.org/content/jour...