Nick Sanderson

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...

Bats from the Colombian Caribbean Reveal a new subtype of Influenza A (H18N12) http://biorxiv.org/cgi/content/short/2024.08.25.609627v1

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have lar...

Our latest paper evaluating nanopore R10.4.1 sequencing for de novo assembly of bacterial pathogen genomes has been published in Microbial Genomics. We may no longer need hybrid assemblies
www.microbiologyresearch.org/content/jour...

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

New preprint: reprocessing 5million SARS-CoV-2 genomes to remove systematic errors (+thereby improve the phylogeny) and improve representation of genomes from the Global South. Huge amount of work esp. from Martin Hunt @angieshinrichs.bsky.social +collabs

www.biorxiv.org/content/10.1...

Plasmids are extrachromosomal replicons. When taken as a whole, plasmids are typically AT-rich compared to the host chromosome. However, the GC-content of in... William Matlock | Gene essentiality shapes plasmid GC-content

🌟 Dive into the fascinating world of plasmid evolution with Will Matlock's brilliant talk from our Oxford Pop Up event, now on YouTube 👉
'Gene essentiality shapes plasmid GC-content' youtu.be/snMchJCJQ5U

@wtmatlock.bsky.social

#ECR #MicrobialGenomics #MNGPopUp #Plasmids

Reviewer help please- looking for someone with expertise in using bioinformatic analysis of ribosomal protein (L7/L12) structures to predict B- and T-cell antigenic epitopes as potential vaccine targets

First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset)
www.biorxiv.org/content/10.1...
#microsky

Thanks! It all started in your lab 😀

90% of slack usage is deciding when to go for lunch

Get any sleep?

At least you have network ports, I hope they work

www.youtube.com/watch?v=X5pM...

Every. time.

Another preprint, this time on the accuracy of R10.4.1/kit14 using the new methylation aware basecalling model.
TL;DR we think it’s as good as hybrid assemblies now

www.biorxiv.org/content/10.1...

New preprint on our work using SureSelect target enrichment to sequence N. gonorrhoeae direct from sample www.medrxiv.org/content/10.1...