Hi, currently looking at a #phage proposal. Does anybody know a #bioinformatics tool that can search for virus sequences in #metagenome assemblies?

New NIOO publication: Impact of the fungal #pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root #microbiome. #rhizosphere #endosphere #metagenome #metatranscriptome
https://doi.org/10.1186/s40793-023-00524-7

Another windy, rainy morning in Germany but at least 30,000 of my metagenomes have been annotated since yesterday. Only 430,000 more to go.. ⏰ #microbiome #metagenome

According to the new #metagenome paper, #viruses / #phages of non-aquatic environments only outnumber cells by about two-fold (major capsid protein and universal SCGs used as markers). So the new estimation of virus/phage count might be far closer to cells. Interesting. #microbiology

https://www.nature.com/articles/s41396-023-01431-y

#Viruses infecting #bacteria & #archaea are often identified via metagenomics, but information regarding #phage hosts is lost. @simroux_virus &co present iPHoP, a new tool to maximize host prediction for #metagenome-assembled virus genomes #PLOSBiology https://plos.io/41A5QvG

#Viruses infecting #bacteria & #archaea are often identified via metagenomics, but information regarding #phage hosts is lost. @simroux_virus &co present iPHoP, a new tool to maximize host prediction for #metagenome-assembled virus genomes #PLOSBiology https://plos.io/41A5QvG

🚨 New pipeline release! 🚨

🦠 The nf-core/mag v2.3.0 (Red Cow) pipeline for #metagenome assembly and binning now includes CheckM and GUNC for improved #MAG completeness esimates, CONCOCT as an additional binner, and improved CAT reporting, alongside a range of bug fixes and improvements!

Thanks as always to all the contributors!

@nf_core

https://t.co/RaSuR1r8G0

"...high-resolution spatio-temporal #sampling of the spring bloom in a #freshwater reservoir and describe a multitude of previously unknown taxa using #metagenome-assembled genomes of #eukaryotes, #prokaryotes, and #viruses in combination with a broad array of methodologies." https://pubmed.ncbi.nlm.nih.gov/36698172/

"...high-resolution spatio-temporal #sampling of the spring bloom in a #freshwater reservoir and describe a multitude of previously unknown taxa using #metagenome-assembled genomes of #eukaryotes, #prokaryotes, and #viruses in combination with a broad array of methodologies." https://pubmed.ncbi.nlm.nih.gov/36698172/

From @plos #Computational #biology | Ten simple rules for investigating (meta)genomic data from environmental ecosystems | #TSRPLOSCB #metagenome #editorial #bioinformatics | I like their Fig. 1, and I like all of the rules, but I am partial to Rule 7: Databases are the key to everything | https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010675

@raliegar unfortunately could not make it to the #MikrobioGune meeting here in Bilbao, but I'm proud to stand in and present her poster below about our daring hunt for #omega3 and other #PUFA producing microbes in the #mesopelagic and other marine strata, using public and in-house #metagenome s.

Deep divergence and genomic diversification of gut #symbionts of neotropical stingless bees | bioRxiv

https://www.biorxiv.org/content/10.1101/2022.12.08.519137v1

#bees #microbiome #metagenome

Fantastic talk from @wwood@twitter.com about their Sandpiper tools for #metagenome analysis https://sandpiper.qut.edu.au/ and how they have been using it for strain level metagenomics