Elviz – exploration of metagenome assemblies with an interactive visualization tool

Cantor, Michael; Nordberg, Henrik; Smirnova, Tatyana; Hess, Matthias; Tringe, Susannah; Dubchak, Inna

doi:10.1186/s12859-015-0566-4

Elviz – exploration of metagenome assemblies with an interactive visualization tool

Journal Article · Tue Apr 28 00:00:00 EDT 2015 · BMC Bioinformatics

DOI:https://doi.org/10.1186/s12859-015-0566-4· OSTI ID:1626759

Cantor, Michael ^[1]; Nordberg, Henrik ^[2]; Smirnova, Tatyana ^[2]; Hess, Matthias ^[3]; Tringe, Susannah ^[2]; Dubchak, Inna ^[2]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); DOE/OSTI
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of California, Davis, CA (United States)

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. 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. 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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626759

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 16; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation Laczny, Cedric C.; Kiefer, Christina; Galata, Valentina Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx348	journal	May 2017
Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies Güllert, Simon; Fischer, Martin A.; Turaev, Dmitrij Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0534-x	journal	June 2016
Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies Delmont, Tom O.; Eren, A. Murat PeerJ, Vol. 4 https://doi.org/10.7717/peerj.1839	journal	January 2016
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