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
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
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
Previous studies of extrachromosomal circular DNA (eccDNA) in plants are based on short-read sequencing and cannot efficiently identify their full-length, generated from transposable elements. This study uses long-read sequencing to obtain a comprehensive map of full-length eccDNAs from Arabidopsis and identifies their genomic origins and epigenetic regulation.
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
Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypomethylated plants. It is, however, well-known that TEs can also be active in the soma, although the high-confidence detection of somatic events has been challenging. Results Here, we leverage the high accuracy of PacBio HiFi long reads to evaluate the somatic mobility of TEs in individuals of an A. thaliana non-reference strain lacking activity of METHYLTRANSFERASE1 (MET1), a major component of the DNA methylation maintenance machinery. Most somatically mobile families coincide with those found in germline studies of hypomethylated genotypes, although the exact TE copies differ. We also discover mobile elements that had been missed by standard TE annotation methods. Somatic TE activity is variable among individual plants, but also within TE families. Finally, our approach points to the possible involvement of alternative transposition as a cause for somatic hypermutability in a region that contains two closely spaced VANDAL21 elements. Conclusions Long-read sequencing reveals widespread TE transposition in the soma of A. thaliana hypomethylated mutants. Assessing somatic instead of germline mobilization is a fast and reliable method to investigate different aspects of TE mobility at the single plant level.
Pore-C was super helpful to bring a good Victoria cruziana genome sequence assembly to chromosome-scale: N50 increased from 44 to 300 Mbp.
nf-core
Boas Pucker
Amelia Cervera 🧬