Andries van Tonder

I'm very pleased to be back at Noguchi Memorial Institute for Medical Research helping run our "Working with Bacterial Genomes" course for the first time outside of Cambridge. A big thank you to the funding provided by GIZ, CRIT, Dr Prince Asare and the ongoing support from NMIMR

The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: training.cam.ac.uk/bioinformatics…

Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis genome.cshlp.org/content/34/10/… 🧬🖥️ github.com/bacpop/ska.rust 🦀

We will be running the next in person iteration of our bacterial genomics course in Cambridge at the beginning of July. Please let anyone who may be interested know. training.cam.ac.uk/bioinformatics…

🚨 Out now!🚨 Our #OneHealth study on multidrug-resistant #Shigella spread between humans & primates in Albuquerque is live @NatureComms 👉 nature.com/articles/s4146… Massive thanks to @NMDOH , @UNMHSC , @LosAlamosNatLab , @abqbiopark , @cabq & lead author @rovinsarahtonin ! 🔬🦠

Ever wondered what a snapshot of single cell/spatial dataset can reveal? scCellFie - a scalable tool that goes beyond gene expression, making metabolic analysis possible 3-2-1 Say GENES🤳 BioRxiv doi.org/10.1101/2025.0… TRY NOW sccellfie.readthedocs.io #DataScience #Bioinformatics

Don't forget to apply to work with @OxfordBiology @IneosOxford on #Mtb #Bioinformatics and Microbiology. Deadline soon ! @UniofOxford #Mtuberculosis #Jobs #PostDoc #Biology #Microbiology #UkJobs

We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue doi.org/10.1093/nar/gk… Easy to use, no registration, fast, various visualizations, in sync with Bakta CLI: bakta.computational.bio (1/5)

Tuberculosis in found dead badgers at the edge of the expanding bovine tuberculosis epidemic. Published: 27 March 2025 nature.com/articles/s4159…

Another week and more pipeline updates, this time my two assembly pipelines: Illumina: github.com/avantonder/ass… ONT: github.com/avantonder/ass… Have a try and let me know what you think

Just updated seqkit, csvtk, taxonkit, and rush. Click to see changes: - github.com/shenwei356/seq… - github.com/shenwei356/tax… - github.com/shenwei356/csv… - github.com/shenwei356/rus…

If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc: sanger.wd103.myworkdayjobs.com/WellcomeSang... Incredibly exciting datasets on host-microbe interactions in the lung. Pls RT and reach out if you are interested

Super happy to see the new @nextflowio training videos up online. This is a brand new course for beginners, called #Hello #Nextflow - we've run it a few times and the feedback has been great! Material is at training.nextflow.io and videos on YouTube: youtube.com/watch?v=G3CV-F…

I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback. github.com/avantonder/bac… github.com/avantonder/bac…

🦠🧬🖥️ New Bakta DB v6.0 released! After a year, it was time for a Bakta database update - and it's a huge one: - IPS: 330.9M - PSC: 135.3M - PSCC: 37M doi.org/10.5281/zenodo… 👇 1/6

Inference of multiple mergers while dating a pathogen phylogeny academic.oup.com/sysbio/article…

A metagenomic perspective on the microbial prokaryotic genome census | Science Advances science.org/doi/10.1126/sc…

CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes bmcbioinformatics.biomedcentral.com/articles/10.11… 🧬🖥️🧪 #Rstats github.com/gmoro-bioecope…

Need to visualize multi-dimensional categorical data in R? ggalluvial, an extension of ggplot2, makes it easy to create alluvial diagrams and Sankey plots, helping you uncover patterns and flows across categories. ✔️ Plot alluvial diagrams to represent relationships between categorical variables. ✔️ Create Sankey plots to visualize flows and transitions. ✔️ Customize aesthetics, including colors, labels, and node arrangements. ✔️ Handle both wide and long-format data sets with ease. Whether you're analyzing survey responses, tracking user behavior, or exploring categorical trends, ggalluvial simplifies the creation of clear and informative visualizations. The visualization shown here is taken from the package website: corybrunson.github.io/ggalluvial/ Learn more about ggplot2 and its extensions in my online course "Data Visualization in R Using ggplot2 & Friends." Click this link for detailed information: statisticsglobe.com/online-course-… #VisualAnalytics #ggplot2 #Rpackage #DataVisualization #datascienceeducation #database #rstudioglobal #RStats #DataAnalytics #tidyverse

Visualizing gene structures in R? gggenes, an extension of ggplot2, simplifies the process of creating clear and informative gene diagrams, making genomic data easier to interpret and share. ✔️ Plot gene arrows to represent gene locations and orientations. ✔️ Visualize genomic features, including transcripts and operons. ✔️ Customize labels, colors, and layouts for clear presentations. Whether you're working on genome annotation, comparative genomics, or molecular biology research, gggenes provides a flexible and user-friendly way to display complex gene structures with clarity. The visualization shown here is taken from the package website: cran.r-project.org/web/packages/g… For a deeper dive into creating impactful visualizations with ggplot2 and its extensions, don’t miss my online course "Data Visualization in R Using ggplot2 & Friends!" Click this link for detailed information: statisticsglobe.com/online-course-… #RStats #Rpackage #DataAnalytics #ggplot2 #datastructure #DataViz