💾 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...
Amazing!
Do you have an interest in AMR and OneHealth?
Then apply for our PhD, exploring the prevalence of resistance of Enterobacterales across poultry farms, fresh produce systems, and wastewater treatment plants.
www.gre.ac.uk/docs/rep/com...
#AMR #OneHealth #PhD #Microbiology #Genomics #FoodSafety
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
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-...
The 👏 point 👏 of 👏 vaccination 👏 is 👏 that 👏 we 👏 don’t 👏 have 👏 to 👏 urgently 👏 treat 👏 severely 👏 ill 👏 children
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?
If so, you might this little project: github.com/rrwick/conda...
Graphic includes an image of vegetables, meat and eggs in petri dishes ready for closer inspection. The text is: Applied Food Safety and Quality Management MSc/PGDip. Our MSc programme will equip you with the skills to navigate the complexities of food safety and quality control, preparing you to address pressing issues and ensure an adequate, safe food supply.
Master the art of food safety and quality management! #StudyatNRI
Our MSc in Applied Food Safety and Quality Management offers a comprehensive approach, ensuring safe and high-quality food for consumers.
#FoodSafety
www.nri.org/study/postgr...
I am beyond excited to share that you can now apply to observe a @wellcometrust.bsky.social #DiscoveryResearch shortlisting Committee! If you plan to apply to us in the next 2 years, apply to be an Observer now to better understand what happens once you click submit! wellcome.org/grant-fundin...
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
Would it be great to have a tool that harmonises all the different AMR prediction tool outputs? We agree and outline it in this paper!
www.biorxiv.org/content/10.1...
GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis journals.asm.org/doi/full/10.... #jcampubs
Reposting our work on sylph, a new fast and precise metagenomic profiler.
Check it out here github.com/bluenote-157...
Tldr: profile against 85k prokaryotes and 2.9 million viruses in a minute and 16 gb of ram. Seems to be accurate at the species level, ANI output too!
Blueskiers! I am starting a Practical bioinformatics for biologist course from scratch this spring semester focused on microbes 🦠 🧫. I am putting the finishing touches on it but want to make sure it’s well rounded. It’ll be heavily hands on. But anyone have lectures they’re willing to share?
New paper by Pat Schloss about rarefaction is definitely worth a read for microbiome aficionados
journals.asm.org/doi/10.1128/...
AMR folks! Come join a great conference: Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (13-15 March 2024).
Awesome line-up of speakers.
Bursary deadline 19 December.
Abstract deadline 16 January.
coursesandconferences.wellcomeconnectingscience.org/event/antimi...
Workshop‼️ One Health and antimicrobial resistance: role of antibiotics, antimicrobial peptides and biocides
29 & 30 January 2024 in Berlin, Germany and online
We're coming to the University of Oxford on the 7th March 2024 from 9.30 to 16.30. Cool science, networking, free lunch, friendly atmosphere. A microbial genomics conference series, Register FREE https://linktr.ee/microbesng. There is an image of the Magdalen college buildings.
📢MicrobesNG POPUP Conference is coming to Oxford!
This is a FREE Microbial Genomics conference 7th Mar🦠🧬
We're accepting abstracts for talks now! Focus on ECRs. Please repost!
Submit abstract by 6th Dec 👉 www.surveymonkey.co.uk/r/Oxford_Abs...
Organised by @rwheatley8.bsky.social
#MNGPopUp #ECR
Interesting preprint by Edwin et al. of possible interest:
An In-depth Evaluation of Metagenomic Classifiers for Soil Microbiomes
www.researchsquare.com/article/rs-3...
The hacked the @nanopore sequencer to read amino acids and PTMs along protein strands. This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification 🧬🧪🤯
www.biorxiv.org/content/10.1...
🚨 #DataVisualization in R for Scientists! 🔥
#DataViz protocols: An introduction to data visualization protocols for wet lab scientists#
A fantastic resource from @joachimgoedhart.bsky.social 🙏👏👍
joachimgoedhart.github.io/DataViz-prot...
Today has been a good day in the lab 😀 My first Nanopore sequencing run is on!
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Only been here 5 minutes and I’m already liking what I see! 😊