Background: A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables.
Results: Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools.
Conclusions: Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190407 | PMC |
| http://dx.doi.org/10.1186/1471-2105-12-385 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data.
NAR Genom Bioinform
December 2024
Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, 225 North Avenue NW, Atlanta, GA, 30332, USA.
Dimension reduction (DR or embedding) algorithms such as t-SNE and UMAP have many applications in big data visualization but remain slow for large datasets. Here, we further improve the UMAP-like algorithms by (i) combining several aspects of t-SNE and UMAP to create a new DR algorithm; (ii) replacing its rate-limiting step, the K-nearest neighbor graph (K-NNG), with a Hierarchical Navigable Small World (HNSW) graph; and (iii) extending the functionality to DNA/RNA sequence data by combining HNSW with locality sensitive hashing algorithms (e.g.
View Article and Find Full Text PDFThe microbiome and the eye: a new era in ophthalmology.
Eye (Lond)
December 2024
Corneoplastic Unit, Queen Victoria Hospital, East Grinstead, RH19 3DZ, UK.
The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases.
View Article and Find Full Text PDFAnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.
F1000Res
December 2024
Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, New York, USA.
Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows.
View Article and Find Full Text PDFCase report: Unveiling the silent threat in the ICU - a case of disseminated invasive aspergillosis in a patient with fulminant myocarditis.
Front Immunol
December 2024
Fourth Department of Critical Care Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, Fujian, China.
Invasive aspergillosis (IA) significantly increases mortality in critically ill patients in the ICU and its occurrence is closely related to immunocompromise. Dissemination of IA is easily misdiagnosed and mistreated due to its ability to invade multiple systems throughout the body and lack of typical clinical manifestations. In this case, a 25-year-old previously healthy woman was hospitalized with fulminant myocarditis and treated with veno-arterial extracorporeal membrane pulmonary oxygenation (VA-ECMO) support and intravenous acyclovir, high-dose methylprednisolone, and immunoglobulin.
View Article and Find Full Text PDFMicrobiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.
Appl Environ Microbiol
December 2024
Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
Article Synopsis
- Wood-fall micro-ecosystems in the deep ocean were studied to understand the diversity and assembly of bacteria and fungi and their biogeochemical functions.
- Results indicated that habitat heterogeneity influenced microbial communities, with bacterial communities in specific regions being affected by dispersal limitations while fungi were influenced by homogenizing dispersal.
- The study concluded that bacteria had a greater potential for key metabolic processes like sulfur and methane cycling, while certain fungi showed a strong ability to degrade lignocellulose, highlighting the complex interactions in these micro-ecosystems.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!