de.NBI & ELIXIR Germany1d ago

🧬 Next @deNBI training course: Nanopore Sequencing 101: 🧬

Join us for a deep dive into ONT technology! 🚀

📅 30 June - 2 July 2026
📍 Bielefeld, Germany
💻 Focus: Linux basics, Library Prep, de.NBI Cloud, Genome Assembly & Metagenomics.
🛠️ Tools: Dorado, Flye, CheckM, Bakta & more!

Perfect for PhDs & Postdocs. No prior bioinformatics knowledge required 🐧

Register here: https://www.denbi.de/training-courses-2026/2071-nanopore-sequencing-101-from-library-prep-to-genomics-and-metagenomic-analysis

#Genomics #Bioinformatics #Nanopore #ONT #Bielefeld #deNBI #ScienceTraining #Metagenomics #Linux

nf-core3d ago

Pipeline release! nf-core/mag v5.4.2 - mag 5.4.2 - Yellow Frog patch!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.2

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Release mag 5.4.2 - Yellow Frog patch · nf-core/mag

Added #1006 - Add citations and references texts in the utils_nfcore_mag_pipeline subworkflow (by @dialvarezs) Changed #1000 - Update GUNC modules and enable the tool in tests (by @dialvarezs) #...

GitHub
Carlos RedingMar 23

Hi everyone 🖖

If you are thinkging about using #nanopore for genomic surveillance in #hospitals, but don't have the #bioinformatics nor command-line skills, don't let that put you off.

'Modernising Medical Microbiology', at @NDMOxford in #Oxford, has developed `OxBreaker': a graphical tool that can help identify budding #outbreaks by #healthcare professionals without having to upload your data to external servers and compromise patient privacy. Worth a read 👇

https://www.biorxiv.org/content/10.64898/2026.03.18.709804

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing

Real-time genomic surveillance may mitigate the spread of health-care-associated infections, but whole-genome sequencing costs and the need for specialised expertise constrain its wide implementation in public health. Here we present ‘ OxBreaker ’, an automated and species-agnostic pipeline optimised for the high-resolution analysis of bacterial and plasmid genomes sequenced via Oxford Nanopore Technologies (ONT). ‘ OxBreaker ’ streamlines the transition from raw reads to phylogenetic inference through automated reference selection and high-accuracy variant calling. It is accessible via a graphical user interface (GUI) that can be easily installed locally and operated by non-specialists. Benchmarking against technical and biological replicates of high-priority pathogens demonstrates high accuracy, with false positive variant rates reduced to 0–4 single-nucleotide polymorphisms (SNPs) for common species. We further validated the pipeline by accurately characterising previously published clonal and plasmid-mediated outbreaks, reproducing established phylogenies with improved accessibility. By providing a stable, scalable, open-source offline-compatible solution that matches the resolution of short-read platforms while maintaining the speed of long-read technology, ‘ OxBreaker ’ is designed to facilitate the adoption of local, real-time genomic surveillance for frontline infection prevention and control. ### Competing Interest Statement The authors have declared no competing interest. NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, NIHR207397 NIHR Biomedical Research Centre, Oxford, GB

bioRxiv
nf-coreMar 12

Pipeline release! nf-core/mag v5.4.1 - mag 5.4.1 - Yellow Frog patch!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.1

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

nf-coreMar 9

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

PuckerLabMar 7

We are delighted to welcome Hannah to our group. She will conduct long-read sequencing to explore plant genomes. We are excited to have her on board and look forward to amazing discoveries ahead!

https://www.izmb.uni-bonn.de/en/pbb/team

#PlantGenomics #LongReadSequencing #Bioinformatics #Nanopore #PlantScience #TeamScience
@boas_pucker

de.NBI & ELIXIR GermanyFeb 24
🔬✨ Tool of the week: #Metagenomic data analysis made easy!
🚀 The Metagenomics-Toolkit offers a complete workflow: from raw #Illumina or #Nanopore reads 📈 to taxonomic 🦠 and functional 🧬 insights.
📊 Reproducible, publish-ready results.
Ready to boost your research? 🌍📝 For more information see:
https://www.denbi.de/services-according-to-service-centers/1991-metagenomics-toolkit-scalable-data-agnostic-workflow-for-the-automated-analysis-of-metagenomic-datasets
nf-coreFeb 16

Pipeline release! nf-core/taxprofiler v1.2.6 - v1.2.6 - Bouncy Basenji Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.6

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Release v1.2.6 - Bouncy Basenji Patch · nf-core/taxprofiler

Added #678 Included metaval.config to generat input files for genomic-medicine-sweden/metaval (added by @LilyAnderssonLee) #655 Added nf-tests for test profile (added by @sofstam) Fixed #674 Fix...

GitHub
Mihail ZdravkovFeb 11

Does anyone know if an NVidia RTX 4060 can handle an Mk1D MinION with runtime basecalling? ONT's documentation says that the minimum requirement is an RTX 5060, but this sounds a bit crazy. And the difference between the two GPUs is not that big I think.

Also, this will mostly be for dRNA-seq, where we basecall after the run, so would it be okay to run two MinIONs in parallel (without basecalling)?

#nanopore #nanoporeSequencing #OxfordNanopore

nf-coreFeb 2

Pipeline release! nf-core/mag v5.4.0 - mag 5.4.0 - Yellow Frog!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.0

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics