Thrilled to see this preprint finally out! This was an exciting collab and massive effort building a workflow for rapid ID of bacterial & fungal pathogens and #AMR determinants in bloodstream infections using @nanoporetech.com sequencing www.biorxiv.org/content/10.6... 🧵1/4

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

Check out our ChroQueTas tool (github.com/nmquijada/Ch...) and get ready to screen AMR in your fungal genomes by using FungAMR info!

The final installment in our plasmid surveillance trilogy is now out in @microbiologysociety.org #MGen! We examined NDM plasmid distribution across years of Canadian surveillance data, and found NDM plasmids are super diverse www.microbiologyresearch.org/content/jour... 1/8

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Citrobacter freundii ain't ever been a friend of ours... now becoming even more hostile! #IDSky #ClinMicro #AMR #MedSky @lancetmicrobe.bsky.social www.thelancet.com/journals/lan...

Enjoying #APBHM25 - lots of super talks and excited to try out all the new tools! I'm virtually presenting poster # 115 on our lab & bioinf workflow to rapidly identify bacteria & fungi organisms and AMR determinants from positive blood cultures, check it out here: github.com/lerminin/abp... 1/3

Happy to see this out - please try my code and break it! Also come see me at #ABPHM25 in the showcase today, where I’m presenting AMRGen, an R package for combining and exploring AMR geno pheno data. It was used to help make many of these rules interpretamr.github.io/AMRgen/

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...

🦠🧬🖥️ 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/zeno... 👇 1/6

A work that started 10y ago with a simple experiment with a curious result. Great to see it finally published. Massive effort by @nic-ler.bsky.social and Andrew Cameron! Happy to have contributed to this!