Ali Hakimzadeh

New #metagenome assembly comparison of PacBio, ONT, and Illumina in human gut #microbiomes.

- "HiFi generated more cMAGs than ONT at every depth with either assembly method"
- "HiFi cMAGs had significantly higher completeness and lower contamination than ONT"

doi.org/10.1016/j.ce...

ERC grant will support placement of tens of thousands of previously unknown fungi on evolutionary tree Leho Tedersoo, Professor of Mycorrhizal Studies at the University of Tartu, has received the Advanced Grant from the European Research Council to systematise and describe members of the 95% majority o...

Read more from here: ERC grant will support placement of tens of thousands of previously unknown fungi on evolutionary tree ut.ee/en/news/erc-...

EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we mis...

Looking for a database to functionally assign your 18S (terrestrial)data to trophic groups? Look no further! Our article is published here: doi.org/10.1111/1755... and you can find the database here as a R package: github.com/lentendu/Euk... #soils #eukaryotes #protists #fungi

GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions a simple tool for listing conda environments with descriptions - rrwick/condaenvlist

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?

If so, you might this little project: github.com/rrwick/conda...

The Impact of Oil Palm Plantations and Pastures on Benthic Prokaryotic and Fungal Communities in Tropical Streams The expansion of oil palm plantations and cattle grazing lands has a detrimental impact on freshwater ecosystems, causing ecological degradation and biodiversity loss in the tropics, although litt...

While oil palms and pastures alter tropical stream microorganisms, riparian buffers offer a lifeline. 🚑💧 Saving biodiversity could depend on protecting these green corridors.

🔗 Read more: doi.org/10.1111/fwb....
#eDNA #FreshwaterBiology #conservation

EUKARYOME v1.9.3 now available in eukaryome.org

A special release of long reads of marine microeukaryotes

I started an #eDNA starter pack as one didn’t exist yet. Feel free to message me to get your name added. Open to all! go.bsky.app/U2vgV5Q

End-to-end simulation of nanopore sequencing signals with feed-forward transformers https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae744/7930676 🧬🖥️🧪 https://github.com/ZKI-PH-ImageAnalysis/seq2squiggle

New preprint led by Ruben Gonzalez-Miguens for a new coi database that should be useful to annotate metabarcoding datasets with protists.

www.biorxiv.org/content/10.1...