Andries van Tonder

A cross-environment comparison of nontuberculous mycobacterial diversity https://www.biorxiv.org/content/10.1101/2025.08.04.668438v1

Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes - Nature Genetics Analysis of synteny blocks and genomic rearrangement patterns of 178 newly sequenced and 64 publicly available complete genomes of Yersinia pestis highlights the impact of key variations on genes invo...

If ever a species needed a large scale long-read genomics project it is Y. pestis. Great paper!

www.nature.com/articles/s41...

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update) Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...

The new version of MetaPhlAn v4.2.2 released!

📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs

Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...

Spinger Nature Discovers MDPI – The Strain on Scientific Publishing Home page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro

New from The Strain Team:
🎊 Springer Nature Discovers MDPI 🎊

Springer Nature has spawned a copycat journal series called "Discover" mimicking #MDPI journal titles and citation behaviours. We even made a browser game to prove it (see 🔗).

Gross! 😀 1/n

#ResearchIntegrity #SciPub #AcademicSky

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace.
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...

New blog post!
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules

We will be running the next in person iteration of our bacterial genomics course in Cambridge at the beginning of July

www.training.cam.ac.uk/bioinformati...

Please let anyone who may be interested know.

Autocycler: long-read consensus assembly for bacterial genomes Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
(1/6)

Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat? Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been ove...

🥁 NEW:

Commentary in @cellcellpress.bsky.social!

by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger

www.cell.com/cell/fulltex...

1/4

Autocycler: long-read consensus assembly for bacterial genomes Motivation: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using ...

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

Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)

github.com/rrwick/Autoc...

Wonder the "chemicals" between gut bug pairs? Check out this new preprint lead by @skamrad.bsky.social and am honored to contribute!

Plasmid–bacteria associations in the clinical context Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have inv...

New opinion paper from the lab!

www.cell.com/trends/micro...

The landing page of the course "ggplot2 uncharted" with the title teasing it with "Master Data Visualizations with ggplot2".

Excited to launch "ggplot2 [un]charted" with @yan-holtz.bsky.social! 🎉

An online course to master #ggplot2 with exercises, quizzes, and modules—and hands-on code running in your browser!

Still WIP—sign up now for a limited discount:
👉 www.ggplot2-uncharted.com

#rstats #DataViz #DataVisualization

🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩‍💻

📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!

#bioinformatics #opensource #STEMeducation

With {tidylog}, you see friendly messages like: summarise: now 3 rows and 3 columns, ungrouped filter: removed 2 rows (67%), one row remaining

With {tidylog}, you see friendly messages like:

summarise: now 3 rows and 3 columns, ungrouped

filter: removed 2 rows (67%), one row remaining

✨ It’s like having a gentle co-pilot, helping you track what each step is doing — super useful for debugging and learning!

Hidden in plain sight: Bacterial genomes reveal thousands of lytic phages with therapeutic potential Phages are typically classified as temperate, integrating into host genomes, or lytic, replicating and killing bacteria. Lytic phages are not expected in bacterial genome sequences, yet our analysis o...

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

Searching for lytic phages in bacterial genome assemblies ..!

EMBO Practical Course Methods for infectious disease modelling using genomics 14 - 19 September 2025 Hinxton, United Kingdom

You have until 25 May to apply for this @embo.org Practical Course introducing concepts, methods and tools for carrying out infectious disease modelling using genomics www.ebi.ac.uk/training/eve...

There is some financial assistance provided by EMBO - please see the course website for info

🧪🧬🖥️🦠🧫

High frequency body site translocation of nosocomial Pseudomonas aeruginosa Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but...

Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander
www.biorxiv.org/content/10.1...

Global genetic structure of human gut microbiome species is related to geographic location and host health The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

Out now in Cell! Thrilled to share our recent study on global analysis of microbial genetic diversity in geography and human health. Congrats @seandreu.bsky.social and all other co-authors. Special thanks go to @cibiocm.bsky.social and lifelines.

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

Bacterial genome structural variation: prevalence, mechanisms, and consequences A vast number of bacterial genome sequences are publicly available. However, the majority were generated using short-read sequencing, producing fragmented assemblies. Long-read sequencing can generate...

Aww look at these trend setters in #microbiology! Interested in the large genome structural variation that isn't accounted for in short read #sequencing & consequences these have, read the latest review by our @emmabeansworth.bsky.social & @gemma-langridge.bsky.social

#academicsky #academicchatter

Brief antibiotic use drives human gut bacteria towards low-cost resistance - Nature Brief ciprofloxacin exposure in humans drives antibiotic resistance evolution in gut bacteria through selective sweeps, particularly involving DNA gyrase mutations, which persist long after exposure a...

New work in Nature shows that a brief 5-day CIP course in (n=60) healthy adults can lead to emergence of AMR in ~10% of ~5600 gut microbial species. Most mutations in gyrA (known FQ hotspots), do not affect fitness & can be detected >10wks (projected to persist >1y)
🔗 www.nature.com/articles/s41...

SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae https://www.biorxiv.org/content/10.1101/2025.04.16.648953v1

argNorm is published now academic.oup.com/bioinformati...

Our latest preprint is out describing amr.watch - a platform for monitoring AMR trends from global genomics data: www.biorxiv.org/content/10.1... (1/6)

A bioinformatician, computer scientist, and geneticist lead bioinformatic tool development—which one is better? AbstractMotivation. The development of accurate bioinformatic software tools is crucial for the effective analysis of complex biological data. This study e

bioinformatician, computer scientist, and geneticist lead bioinformatic tool development—which one is better? academic.oup.com/bioinformati...

Population-scale analysis of inheritance patterns across 858,635 individuals reveals recent historical migration patterns across the North Sea from the Middle Ages to the Industrial Revolution The North Sea's historical migrations have impacted the genetic structure of its neighbouring populations. We analysed haplotype sharing among 858,635 modern individuals from Denmark and Britain to in...

New Preprint klaxon - and calling all Danes+Brits who are interested in genetics+history - a new preprint led by Xiaolei Zhang in my group with Soren Brunak's group about genetic exchange from 1100 to the present day between UK (Britain)+Denmark. Read on for details www.biorxiv.org/content/10.1...

#MicroSky #AMR