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

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...

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

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

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

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...

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...

🌟 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

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

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...

New desk with an actual view and blueskies! Thanks for moving up in the world @scousemicrobe.bsky.social

My new years resolution is to stop accepting review requests from for-profit journals

📢 I have a funded PhD position available in Glasgow. Functional genomics project with vaginal Lactobacillus. Please share www.findaphd.com/phds/project...

Come do a PhD with me at University of Glasgow. 3-year fully funded PhD for UK students. Friend to Foe: Colonisation as an Entry Point for S. aureus Infectionhttps://www.findaphd.com/phds/project/fully-funded-friend-to-foe-colonisation-as-an-entry-point-for-staphylococcus-aureus-infection/?p166823

Our work on the 2022-2023 flu season is out as preprint now www.medrxiv.org/content/10.1...

We're hiring a senior bioinformatician. Come and work with us bit.ly/mmm_sbio

Does VS code ever not need to update to install updates?

If you want to get people back into offices, have very good, subsidised childcare next to the office. Thats 8 weeks in a row I've been in everyday. As a bioinformatician, I haven't done that since 2015!

New preprint! I will try to keep this summary lay-friendly. Recently a viral outbreak started in Cyprus with an unusually high number of cats showing clinical signs of feline infectious peritonitis (FIP), and it is estimated that over 8000 cats had died by mid-July. www.biorxiv.org/content/10.1...

We're hiring a junior research software engineer. Come and work with us, we have a coffee machine bit.ly/mmm_rse

TIL you can copy a file to the server by dragging and dropping it into the explorer pane of visual studio. Great feature, especially when your server admins disabled RSA keys and demands two-factor authentication for rsync!

I'm recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call!

Why have I not set up IGV viewer as a webapp on a server before. This is amazing, I can quickly see all the bams output from our flu workflow and check positions, drops in coverage.