Explaining in simple terms the two main results achieved by our #metagenomic classifier #Slacken - scaling independently of RAM, and sample-tailored libraries. https://jnpsolutions.io/2025/07/03/slacken-published.html

Ancient #DNA reveals 6,000 years of the lives of #Antarctic #penguins.

#metagenomic #sediment #sedaDNA #Pygoscelis

https://phys.org/news/2025-03-ancient-dna-reveals-years-antarctic.html

Next @deNBI #training course:
Joint @NFDI4Microbiota & de.NBI #Metagenomic Training Course 2025 (Braunschweig, 1-3 April). For more information see: https://www.denbi.de/training-courses-2025/1856-joint-nfdi-de-nbi-metagenomic-training-course-2025

🚨 Dear SPAAM community, please fill out this form by Jan 31 to help us gather stats & improve:
https://forms.gle/S1zgzAmsa9wkCa8D7

📝 Reminder: Slack ends in Feb, switch to Element here
https://matrix.to/#/#spaam:archaeo.social

#aDNA #ancientDNA #metagenomic

New #ISEPpapers! Eukaryotic #genomes from a global #metagenomic data set illuminate trophic modes and #biogeography of ocean #plankton https://journals.asm.org/doi/10.1128/mbio.01676-23

#microbes #protists #algae #biology #ecology #genomics #bioinformatics

#VirID: Beyond Virus #Discovery - An Integrated #Platform for Comprehensive #RNA #Virus Characterization, BioRxIV: https://www.biorxiv.org/content/10.1101/2024.07.05.602175v2

We developed VirID, a #software tool specifically designed for discovery & characterization of RNA viruses from #metagenomic data. Basis of VirID is a comprehensive RNA-dependent RNA #polymerase (RdRP) database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization.

Great to be involved in this lovely Water Research paper led by the brilliant Maggie Knight at Bangor University! The paper compares the pros and cons of #qPCR vs #metagenomic approaches for detecting antibiotic resistance genes in wastewater. The comprehensive dataset used in the study was from the the widespread Wales wastewater monitoring. Personally, I'm team metagenomic!
http://doi.org/10.1016/j.watres.2024.121989

I'm looking forward to the @nf_core hackathon and #Nextflow Summit in Barcelona in October!

Is anyone here on Mastodon coming as well (or joining remotely)?

I'll be giving a talk during the summit giving an overview of the #metagenomic and #MicrobialEcology pipeline 'offerings' of #nfcore :)

If you're interested, more info here: https://summit.nextflow.io/2024/barcelona/

#bioinformatics

New technology protects #crops by testing the air for the #DNA of #plant #diseases.

#aeroDNA #metagenomic #pathogens #fungi #agriculture

https://phys.org/news/2024-08-technology-crops-air-dna-diseases.html

#VIRAL #METAGENOMIC #SURVEY OF #CASPIAN #SEALS, BioRxIV: https://www.biorxiv.org/content/10.1101/2024.07.14.603418v1

Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from viral families #Picornaviridae, #Adenoviridae, #Circoviridae, #Herpesviridae, #Papillomaviridae, #Caliciviridae, #Orthomyxoviridae, #Anelloviridae, #Smacoviridae, #Cruciviridae & #Parvoviridae... Among seq. recovered were partial contigs for #influenza B, representing only 2nd molecular identification in marine mammals.

Study reveals the #microbes vital to a healthy Brisbane #River.

#genomics #biodiversity #ecosystem_health #metagenomic #biogeochemical_cycles #eutrophy

https://phys.org/news/2024-06-reveals-microbes-vital-healthy-brisbane.html

Benchmarking #bioinformatic #virus identification tools using real-world #metagenomic data across biomes

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03236-4

First-of-its-kind integrated dataset enables #genes-to-#ecosystems research.

#g2e #microbiome #soil #biome_omics #metagenomic #metabolomic #transcriptomic

https://phys.org/news/2024-04-kind-dataset-enables-genes-ecosystems.html

CZ ID: An #OpenSource cloud-based, no-code platform enabling advanced long read #metagenomic #analysis:

Preprint: https://doi.org/10.1101/2024.02.29.579666
Web: https://czid.org/
GitHub: https://github.com/chanzuckerberg/czid-workflows/tree/main

#DIYbio #lab #instruments #bioinformatics #NGS #genomics #Kraken2 #microbiome

https://www.nature.com/articles/d41586-023-03414-7 #nepal #SHAPU #Gazalina #GazalinaMoth #moth #metagenomic #sequencing #geneticanalysis
10.1038/d41586-023-03414-7
https://doi.org/10.1038/d41586-023-03414-7

See also:
https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(21)00513-1/fulltext

&

https://www.tandfonline.com/doi/abs/10.1080/09286586.2020.1820533

#MetagenomicsMonday 🧬
A large-scale #environmentalDNA #metagenomic study of ancient plant and mammal communities! Researchers analyzed 535 #permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. 🦣🫎🌿🌲 #sedaDNA #ancientDNA #ancientmetagenomics #sedDNA #arctic
https://www.nature.com/articles/s41586-021-04016-x

💻 AMDirT facilitates automated metadata curation and data validation, as well as rapid data filtering and downloading. Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public #ancient #metagenomic #datasets into future analyses. 📊

Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient #metagenomic samples. 🧬 :agar_plate:

🚨#spaamtisch attendees
📈Our first 6 months of
@spaam_community #spaamtisch seminars and regular's table meetings are over. Before starting a new chapter, let us know what you think about the past events by filling this survey form by the 31/08/23

https://docs.google.com/forms/d/e/1FAIpQLSc8NylFBSchrS4KErAJDKvRZTxkLooM0YB-zuSf5yjRvWYtyA/viewform

#aDNA #seminar #ancientDNA #metagenomic #microbiome #bioinformatics #genomics #archaeology #ancient #genetics #data

👇🚨#spaamtisch meeting videos from past seminars are now available on our community YouTube channel! If you missed
Maxime Borry and @jfy133 seminar on AMDirT, a brand new tool for browsing and filtering ancientmetagenomeDir, now you can watch it here
https://youtu.be/evPKxkH4FzI

#aDNA #ancientDNA #bioinformatics #metadata #metagenomic #data #tools #community