If you're interesting in quickly visualising genotypes from a VCF file with a single R command, we've put together a small repo with the function we've been using and tutorial. github.com/JimWhiting91/g…

1) Today's been a hell of a day for plant #pangenomes. In nature.com/articles/s4158… Walkowiak et al analyze up to 16 wheat cultivars to report on the global variation pool accessible to modern breeding

5) Finally, Brinton et al publish in nature.com/articles/s4200… their code and visualization of haplotypes in the context of #pangenomes. All on the same day!

🧬🌱🍻Comparing 20 #barley genomes: Only 17 to 25% of full-length LTR #TransposableElement locations in wild barley shared with any domesticated genotype (high identity thresholds of >=98 %). Makes me curious about TE presence/absence polymorphisms as well.

eLife buys big into a "publish, then review" model of publishing: "From July 2021 eLife will only review manuscripts already published as preprints, and will focus its editorial process on producing public reviews to be posted alongside the preprints." elifesciences.org/articles/64910

The reverse complement of a sequence of nucleotides can be found on a terminal using the 'tr' and 'rev' bash commands #openmethods #minimethods

🌱🧬Very happy to share Nicolas first manuscript: 📚biorxiv.org/content/10.110… She has looked into the #SugarBeet genome and found countless fossils of past #viral infections with #pararetroviruses. For the host, there is one question: Keeping or losing those virus relics? (1/7)

SMALL THREAD: I have seen concerns going round about the theoretical possibility that vaccine mRNA could end up altering our own genomes, and that could cause long term consequences. I will start by saying that this is not a material concern, and will try and explain why. 1/n

Happy to share that a newly discovered plant species was named after Stefan Wanke, one of my academic mentors: #Aristolochia wankeana. Check the Phytotaxa updates paper: mapress.com/j/pt/article/v… ... and an outreach article: scienmag.com/new-plant-spec… #botany @TUD_Science

Our study using Oxford Nanopore ONT sequencing to survey transposable element (TE) insertions and methylation landscapes in human tissues is now in print Molecular Cell. Detailed thread 👇 Open access link: sciencedirect.com/science/articl… Work funded by NHMRC CSL Mater Foundation 1/n

Die #DFG hat die Verlängerung der Initiative #NextGenerationSequencing (#NGS) bis 2023 beschlossen. Aktuell läuft die Begutachtung der dritten Ausschreibungsrunde zu „#Sequenzierkosten in Projekten“. Weitere #Ausschreibungen folgen ➡️ dfg.de/foerderung/inf…

🌱Really happy that we could contribute to the #chromosome biology calendar of the @IPKGatersleben! 🔍Have a look at Nicola Schmidt's image of pararetroviruses along sugar beet's chromosomes (doi.org/10.1101/2020.1…). Thank you to all involved; this is a great initiative!

Peer review ramblings #4: this year I signed all of my journal referee reports and I am glad I did despite the potential drawbacks. It would be great if we lived in a scientific world where we could all be open and accountable to what we say and do.

Please apply - the project is fully funded. Application deadline January 15.

Data structures based on k-mers for querying large collections of sequencing data sets [REVIEW], by Camille Marchet @[email protected] PM @[email protected] @pashadag.bsky.social Rayan Chikhi genome.cshlp.org/cgi/content/lo…

Our next journey into the transcripts of “junk” DNA in plants using Nanopore RNA sequencing. mdpi.com/2223-7747/9/12… Congrats to all who was involved 👏 @maxdudnikov1 Pavel Merkulov Elizaveta Kolganova Murad Andrey Shingaliev [email protected]

The changing face of genome assemblies: guidance on achieving high‐quality reference genomes | Molecular Ecology Resources ow.ly/Yp3z30rp8q5

New in Molecular Ecology Resources: A new tool just out to help illuminate the dark regions of genomes. Introducing 'RepeatProfiler': a pipeline for visualization and comparative analysis of repetitive DNA profiles. Link to study → buff.ly/3aEMgXg

RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles onlinelibrary.wiley.com/doi/10.1111/17… #transposon