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PMID: 26500826 Published · epublish English Journal Article

Anvi'o: an advanced analysis and visualization platform for 'omics data.

PeerJ ·Vol. 3 ·2015-00-00 ·Pages e1319

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO

Abstract

Advances in high-throughput sequencing and 'omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi'o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link 'omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi'o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi'o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large 'omics datasets.

Keywords
Assembly Genome binning Metagenomics Metatranscriptomics SNP profiling Visualization
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Eren A Murat
Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States ; Department of Medicine, The University of Chicago , Chicago, IL , United States.
Esen Özcan C
Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States.
Quince Christopher
Warwick Medical School, University of Warwick , Coventry , United Kingdom.
Vineis Joseph H
Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States.
Morrison Hilary G
Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States.
Sogin Mitchell L
Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States.
Delmont Tom O
Josephine Bay Paul Center, Marine Biological Laboratory , Woods Hole, MA , United States.
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Article Info
Journal
PeerJ
Abbr.
PeerJ
ISSN
2167-8359
DOI
10.7717/peerj.1319
Published
2015-00-00
Epub
2015-00-08
Pages
e1319
Language
English
Region
United States
NLM ID
101603425
PMCID
PMC4614810
Grants
Medical Research Council · MR/M50161X/1 · United Kingdom
External Links
PubMed source DOI: 10.7717/peerj.1319 PMC Full Text View journal details
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