MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes [PDF]
mSystemsWhile numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis.
Clément Coclet +2 more
doaj +4 more sources
MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta‐omics and bioinformatics [PDF]
iMetaThe rapid growth of microbiome research has generated an unprecedented amount of multi‐omics data, presenting challenges in data analysis and visualization.
Defeng Bai +13 more
doaj +3 more sources
Editorial: Advances in viromics: new tools, challenges, and data towards characterizing human and environmental viromes [PDF]
Frontiers in Microbiology, 2023 Mária Džunková +2 more
doaj +4 more sources
DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes
mSystems, 2021 Viromics is becoming an increasingly popular method for characterizing soil viral communities. DNase treatment of the viral size fraction prior to DNA extraction is meant to reduce contaminating free DNA and is a common step within viromics protocols to ...
Jackson W. Sorensen +5 more
doaj +5 more sources
The Human Respiratory Virome in Health and Disease: Interactions, Dysbiosis, and Methodological Challenges. [PDF]
Adv Genet (Hoboken)This article examines how the respiratory virome contributes to health and disease, highlighting its interactions with the host and bacteriome. Key disease associations and present knowledge gaps are outlined. The review discusses challenges in sample collection and preprocessing, and presents future research directions for understanding virome ...
Yao X, Zou X, Cao B.
europepmc +2 more sources
Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain [PDF]
VirusesViromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by the emerging viruses.
Jaime Buigues +5 more
doaj +2 more sources
Computational and Structural Biotechnology Journal, 2015 The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches.
Shirley Bikel +7 more
doaj +3 more sources
Soil Systems, 2020 The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils.
Gareth Trubl +3 more
doaj +3 more sources
Poly-omic risk scores predict inflammatory bowel disease diagnosis [PDF]
mSystemsInflammatory bowel disease (IBD) is characterized by complex etiology and a disrupted colonic ecosystem. We provide a framework for the analysis of multi-omic data, which we apply to study the gut ecosystem in IBD.
Christopher H. Arehart +6 more
doaj +2 more sources
ViOTUcluster: A high-speed, All-in-one pipeline for viromic analysis of metagenomic data. [PDF]
IMetaOmicsViOTUcluster is a user‐friendly, high‐speed, accurate, All‐in‐one solution that streamlines the entire viromic analysis workflow—from raw reads to the generation of viral operational taxonomic units tables, as well as other key viromic analysis tasks.
Liu S +7 more
europepmc +2 more sources