Boas PuckerDec 10

Just wrapped up the “Plant Genome Sequence Assembly and Annotation” course 🌱
Participants dove deep into: processing long-read data, building a genome sequence from scratch, checking assembly quality, and predicting genes. Thanks to everyone who joined and contributed — excited to watch your future discoveries!

https://www.izmb.uni-bonn.de/en/pbb/news#d2025c1

#Genomics #PlantScience #Bioinformatics #GenomeAssembly

@PuckerLab @samnm

galaxyprojectOct 21

My internship experience with assembling genomes and annotating them during a 6 week internship at Freiburg Galaxy.
https://galaxyproject.org/news/2025-07-22-ming-li-internship/

@galaxyfreiburg
#UseGalaxy #GalaxyProject #EOSC #Bioinformatics #Genomics #GenomeAssembly #GenomeAnnotation #TrainingProgram #Internship #Journey #internship #OpenScience #ComputationalBiology #DataScience #ResearchExperience #NextGenScientists

Exploring Genomics with Galaxy: A Six-Week Internship Journey

My internship experience with assembling genomes and annotating them during a 6 week internship

Galaxy-Team der Uni FreiburgOct 21

My internship experience with assembling genomes and annotating them during a 6 week internship at Freiburg Galaxy.
https://galaxyproject.org/news/2025-07-22-ming-li-internship/

@galaxyproject
#UseGalaxy #GalaxyProject #EOSC #UniFreiburg #Bioinformatics #Genomics #GenomeAssembly #GenomeAnnotation #TrainingProgram #Internship #Journey #internship #OpenScience #ComputationalBiology #DataScience #ResearchExperience #NextGenScientists

Exploring Genomics with Galaxy: A Six-Week Internship Journey

My internship experience with assembling genomes and annotating them during a 6 week internship

nf-coreOct 17

Pipeline release! nf-core/bacass v2.5.0 - nf-core/bacass v2.5.0!

Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.5.0

#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

nf-coreJul 21, 2025

Pipeline release! nf-core/genomeassembler v1.1.0 - 1.1.0 - Aluminium Pigeon 'Brass Pigeon'!

Please see the changelog: https://github.com/nf-core/genomeassembler/releases/tag/1.1.0

#genomeassembly #nfcore #openscience #nextflow #bioinformatics

Release 1.1.0 - Aluminium Pigeon 'Brass Pigeon' · nf-core/genomeassembler

Some bugfixes, version and template updates, and internal pipeline refactoring, see changelog for more information. Full Changelog: 1.0.1...1.1.0

GitHub
Melbourne BioinformaticsMay 2, 2025
Melbourne Bioinformatics is hosting a FREE workshop on Hybrid de novo genome assembly using Galaxy. Save the date: Thursday, 5 June 2025, 1:00 PM - 4:00 PM AEST at 21 Bedford Street North Melbourne, VIC 3051. #GenomeAssembly #Bioinformatics
https://www.eventbrite.com.au/e/hybrid-de-novo-genome-assembly-nanopore-and-illumina-using-galaxy-tickets-1232439251979?aff=oddtdtcreator
Hybrid de novo genome assembly - Nanopore and Illumina using Galaxy

Learn how to create high-quality genome assemblies using the powerful combination of Nanopore and Illumina reads.

Eventbrite
LeszekMar 24, 2025
Super cool paper (part of PhD thesis): I thought assembling the genome from raw signal isn't practical, but it seems not possible, but yielding results comparable/better to usual approaches: basecalling followed by de novo genome assembly!
#nanopore #GenomeAssembly
https://arxiv.org/pdf/2410.17801
https://arxiv.org/html/2503.02997v1#Ch7
nf-coreMar 19, 2025

Pipeline release! nf-core/genomeassembler v1.0.1 - 1.0.1 - Aluminium Pigeon!

Please see the changelog: https://github.com/nf-core/genomeassembler/releases/tag/1.0.1

#genomeassembly #nfcore #openscience #nextflow #bioinformatics

Release 1.0.1 - Aluminium Pigeon · nf-core/genomeassembler

Bugfix release addressing bugs discovered after release of 1.0.0 What's Changed use correct genome-size for flye and longstitch by @nschan in #125 Jellyfish singularity container by @nschan in #12...

GitHub
nf-coreNov 18, 2024

Pipeline release! nf-core/bacass v2.4.0 - v2.4.0!

Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.4.0

#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Release nf-core/bacass v2.4.0 · nf-core/bacass

v2.4.0 nf-core/bacass: "Yellow Copper Crayfish" 2024/11/05 Changed #180 Bump version 2.4.0. #169 Refactored long-reads polishing step. #167 Remove params.save_merged as merged reads are not used i...

GitHub
Amelia Cervera 🧬Nov 17, 2024

The complete genome assembly of Nicotiana benthamiana reveals the genetic and epigenetic landscape of centromeres.

#Nicotiana #Centromeres #Transposons #TEs #Satellites #GenomeAssembly

https://www.nature.com/articles/s41477-024-01849-y.epdf?sharing_token=saFx-_W9gEbQ-RGbav1Xc9RgN0jAjWel9jnR3ZoTv0OBMqo8NmgZkxyyQnPBoJcAnjH-u0nveAYuOB-kI0WX2Wq1coFVvmQCrNcNa7eJilzBD7Gnk5_itZCG2Hj0yUl56r9JZxBXpxWByIbAYi-VIHV4YfSGuwEClf1tFqlST2g%3D

The complete genome assembly of Nicotiana benthamiana reveals the genetic and epigenetic landscape of centromeres | Nature Plants

Nicotiana benthamiana is a model organism widely adopted in plant biology. Its complete assembly remains unavailable despite several recent improvements. To further improve its usefulness, we generate and phase the complete 2.85 Gb genome assembly of allotetraploid N. benthamiana. We find that although Solanaceae centromeres are widely dominated by Ty3/Gypsy retrotransposons, satellite-based centromeres are surprisingly common in N. benthamiana, with 11 of 19 centromeres featured by megabase-scale satellite arrays. Interestingly, the satellite-enriched and satellite-free centromeres are extensively invaded by distinct Gypsy retrotransposons which CENH3 protein more preferentially occupies, suggestive of their crucial roles in centromere function. We demonstrate that ribosomal DNA is a major origin of centromeric satellites, and mitochondrial DNA could be employed as a core component of the centromere. Subgenome analysis indicates that the emergence of satellite arrays probably drives new centromere formation. Altogether, we propose that N. benthamiana centromeres evolved via neocentromere formation, satellite expansion, retrotransposon enrichment and mtDNA integration. This study generates and phases the complete genome assembly of a model plant Nicotiana benthamiana, revealing insights into the structure, epigenetic landscape and evolutionary dynamics of its centromeres following allotetraploidization.