Format

Send to

Choose Destination
BMC Bioinformatics. 2015 Apr 28;16:130. doi: 10.1186/s12859-015-0566-4.

Elviz - exploration of metagenome assemblies with an interactive visualization tool.

Author information

1
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. mncantor@lbl.gov.
2
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. henrik.p.nordberg@gmail.com.
3
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. tsmirnova@lbl.gov.
4
University of California at Davis, One Shields Avenue, Davis, CA, 95616-8521, USA. mhess@ucdavis.edu.
5
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. sgtringe@lbl.gov.
6
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. ildubchak@lbl.gov.

Abstract

BACKGROUND:

Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, including both the sequences themselves and metadata describing their abundance, assembly, predicted functional characteristics and environmental parameters. The ability to explore these data visually is critically important to meaningful biological interpretation. Current genomics applications cannot effectively integrate sequence data, assembly metadata, and annotation to support both genome and community-level inquiry.

RESULTS:

Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenomes and their complex metadata. Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation and assembled contig length. Furthermore Elviz enables interactive exploration using real-time plot navigation, search, filters, axis selection, and the ability to drill from a whole-community profile down to individual gene annotations. Thus scientists engage in a rapid feedback loop of visual pattern identification, hypothesis generation, and hypothesis testing.

CONCLUSIONS:

Compared to the current alternative of generating a succession of static figures, Elviz can greatly accelerate the speed of metagenome analysis. Elviz can be used to explore both user-submitted datasets and numerous metagenome studies publicly available at the Joint Genome Institute (JGI). Elviz is freely available at http://genome.jgi.doe.gov/viz and runs on most current web-browsers.

PMID:
25928663
PMCID:
PMC4432942
DOI:
10.1186/s12859-015-0566-4
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center