Lmst

#LongReadSequencing

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

Nice reminder of a great time at Czech University of Life Sciences Prague in Prague 🇨🇿

Teaching Long Read Genomics and exchanging ideas with curious minds is always a highlight. Thanks for the great discussions and warm welcome!

Lecture slides: https://github.com/bpucker/LRG

#Genomics #LongReadSequencing #Academia #Teaching #Bioinformatics #Prague
@PuckerLab

CZU bottle as reminder of a great time in Prague teaching Long Read Genomics (https://github.com/bpucker/LRG)

Pipeline release! nf-core/mag v5.3.0 - mag 5.3.0 - Rainbow Rattlesnake!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.3.0

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

Pipeline release! nf-core/mag v5.2.0 - mag 5.2.0 - Puce Pangolin!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.2.0

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

Pipeline release! nf-core/mag v5.0.0 - mag 5.0.0 - Green Squirrel!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.0.0

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

Pipeline release! nf-core/scnanoseq v1.2.1 - nf-core/scnanoseq v1.2.1 - Zinc Turtle!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.1

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

T-DNA insertions: more surprises than you think 🌱🧬.
PCR can miss extra T-DNAs & complex rearrangements. Long-read sequencing captures the full picture. Still super relevant for plant genomics!
🔗 https://doi.org/10.1186/s12864-021-07877-8
#PlantScience #Genotyping #LongReadSequencing #Arabidopsis @PuckerLab

Genomic rearrangements in the A.thaliana T-DNA line GK-654A12. Source: https://doi.org/10.1186/s12864-021-07877-8

A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation.

#ExtrachromosomalCircularDNA #eccDNA #Transposons #Arabidopsis #MethylationMutants #LongReadSequencing

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003275

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals.

#Transposons #SomaticTransposition #Hypomethylation #MET1 #Arabidopsis #LongReadSequencing

https://link.springer.com/article/10.1186/s13059-025-03691-7

Pore-C was super helpful to bring a good Victoria cruziana genome sequence assembly to chromosome-scale: N50 increased from 44 to 300 Mbp.

https://doi.org/10.1101/2024.06.15.599162

#PlantGenomics #LongReadSequencing #BigData #ONT @PuckerLab

Pipeline release! nf-core/scnanoseq v1.2.0 - nf-core/scnanoseq v1.2.0 - Copper Rhinoceros!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.0

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

🧬 Can advanced sequencing technologies bring clarity to genetic variants once deemed uncertain?

🔗 Combining long-read DNA and RNA sequencing to enhance molecular understanding of structural variations leading to copy gains. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.04.031

📚 CSBJ: https://www.csbj.org/

#Genomics #StructuralVariants #LongReadSequencing #RareDisease #PrecisionMedicine #RNAseq #Nanopore #GeneticDiagnostics #NanoporeSequencing #Transcriptomics

Combining long-read DNA and RNA sequencing to enhance molecular understanding of structural variations leading to copy gains. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.04.031

Pipeline release! nf-core/mag v4.0.0 - mag 4.0.0 - Blue Huemul!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/4.0.0

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

Just wrapped up my talk at the University of Mainz on "Exploring the Specialized Metabolism of Plants with Long Read Sequencing" 🌿🔬 Great to share how nanopore sequencing helps decode complex plant pathways with ecological and biomedical potential. Thanks to the organizers and all who joined the discussion! #PlantScience #Genomics #LongReadSequencing #SpecializedMetabolism #UniversityOfMainz @PuckerLab

Screenshot of slide "Exploring the Specialized Metabolism of Plants with Long Read Sequencing"

Our new paper has surfaced!
We took a deep dive into the bustling microbial metropolis of #LakeBalaton and used some fin-tastic technology to uncover its hidden secrets. Turns out, this lake is teeming with many tiny inhabitants!

So next time you're taking a dip in Lake Balaton, remember you're diving into a whole different kind of culture!

#LongReadSequencing
#Bacterioplankton
You can find more details in the paper:
https://doi.org/10.1038/s41598-025-96558-7

Pipeline release! nf-core/mag v3.4.0 - mag 3.4.0 - Green Gecko!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/3.4.0

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