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Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples dlvr.it/SS6wVW

I have created pharokka, a dedicated fast phage annotation tool inspired by prokka. Pharokka is designed for users who want one-line, rapid, standarised and scalable phage annotations, much like prokka for prokaryotes. github.com/gbouras13/phar…

Myo-, Podo- and Siphoviridae are no more! The age of genomic taxonomy is nigh! To classify our own dsDNA phages, we (Andrew millard) have put together a set of useful files for all classified genera of dsDNA phages and they're available for you too: millardlab.org/2022/08/04/ict…

VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models biorxiv.org/content/10.110…

Why does it exist: host prediction tools have existed for a while, but very few integrated multiple approaches into a single tool. Given the challenges of host prediction, considering multiple approaches for each virus will likely improve performance. That's the basis of iPHoP.

Final transition from morphology to #genome -based #virus #taxonomy after formal removal of Podoviridae, Myoviridae & Siphoviridae! 4 Orders 47 families 98 subfamilies 1199 genera 3600 species Finally a taxonomy reflecting the awesome #phage diversity link.springer.com/article/10.100…

MetaPhlAn 4 is published today OA in Nature Biotechnology Nature Biotechnology nature.com/articles/s4158… We added GTDB output, improved performance and comparative analyses w.r.t. the preprint version. Huge thanks to Aitor Blanco Miguez for the eroic effort and to all Nicola Segata and hutlab

📢only 11 days to go until the early career investigator workshop for #MECFS researchers! Organised by Young European ME Research Group! #Undergrads, #masters students, #PhD students, #postdocs welcome! Also open to researchers investigating other related illnesses #longcovid #Fibromyalgia

Check out the latest preprint manuscript from Carding_lab. We profiled the human gut DNA virome in severe ME/CFS patients & predicted disease-associated bacterial hosts interacting with unique viruses present in ME/CFS microbiomes medrxiv.org/content/10.110… #MECFS #virome

For some more great phage bioinformatic tools (that go great with pharokka) start with Phynteny by Susie Grigson github.com/susiegriggo/Ph… which hopefully will give you annotations for more hypothetical proteins using gene synteny (work in progress but give it a go)! #vom2023

The Tyson lab presents CheckM2, which leverages machine learning for improved estimation of completeness and contamination of metagenome-assembled genomes (MAGs) generated using metagenomics data. Centre for Microbiome Research Alex Chklovski nature.com/articles/s4159…

🆕 Blog! Last month Quadram scientists attended conferences organised by @invest_in_me (Invest in ME Research) 🇪🇺 Research & European ME Research Group (EMERG) sharing their #MyalgicEncephalomyelitis research. Read the blog to find out more & catch Carding_lab giving an overview talk buff.ly/3Qfw2ZK #mecfs #pwme

Our latest paper is live on mdpi.com/1422-0067/24/2… We evaluated the virome of ME patients with the healthy household members, attempting to provide a rationale for future studies to further investigate disease-associated virus–host interactions in ME. #mecfs #severeME #virome

We expanded kallisto to translated alignment (nucleotides <-> amino acids), and used it to detect novel viruses in RNA seq data. The single-cell resolution allowed us to determine whether the presence of these viruses affected host gene expression. 🧵 biorxiv.org/content/10.110…

Don't like p-values? We're presenting a completely new interpretation in the context of clinical trials. With Andrew Gelman, Sander Greenland, guido imbens Simon Schwab and Steve Goodman. Sander Greenland Steven Goodman NEJM Evidence evidence.nejm.org/stoken/default…

Publishing negative results is good for science My latest Editorial for Microbiology Society Access Microbiology, as part of their Negative Results collection. microbiologyresearch.org/content/journa…

SeqKit2: A Swiss army knife for sequence and alignment processing. It suit for nanopore data! #nanopore doi.org/10.1002/imt2.1…

So excited that my first first-author paper is now published in Viruses! In this paper we looked at bias and reproducibility of RNA+DNA faecal virome metagenomic approaches, and compared reverse transcription and PCR amplification using WTA2 and SISPA. 1/4 mdpi.com/1999-4915/17/2…