Anvi’o: An advanced analysis and visualization platform for ‘omics data
A peer-reviewed article of this Preprint also exists.
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Abstract
Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs. Here we introduce anvi’o, an advanced analysis and visualization platform for ‘omics data, and its assembly-based metagenomic workflow. Anvi’o’s interactive interface facilitates the management of contigs and associated metadata for automatic or human-guided identification of genome bins, and their curation. Its extensible visualization approach distills multiple dimensions of information about each contig into a single, intuitive display, offering a dynamic and unified work environment for data exploration, manipulation and reporting. Beyond its easy-to-use interface, the advanced modular architecture of anvi’o as a platform allows users with programming skills to implement and test novel ideas with minimal effort. To demonstrate anvi’o’s capabilities, we re-analyzed a metagenomic time-series data from an infant gut microbiome. Through the anvi’o interface we identified near-complete draft genomes, and explored temporal genomic changes within the abundant microbial populations through de novo characterization of subtle nucleotide variations. We also used anvi’o to re-analyze a collection of datasets from multiple investigators who studied microbial responses to the Deepwater Horizon oil spill. We linked metagenomic, metatranscriptomic, and single-cell genomic data from the water plume, and used the holistic perspective anvi’o provides to identify the draft genome of a previously uncharacterized, active population of Oceanospirillales. We also linked environmental isolates with metagenomes recovered from an oil-contaminated beach, and identified 56 near-complete draft genomes including abundant oil degraders whose functional features suggested an oceanic origin.
Cite this as
2015. Anvi’o: An advanced analysis and visualization platform for ‘omics data. PeerJ PrePrints 3:e1275v1 https://doi.org/10.7287/peerj.preprints.1275v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This article is submitted to Genome Biology on July 30, 2015.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
A. Murat Eren conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Özcan C Esen performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Christopher Quince contributed reagents/materials/analysis tools, reviewed drafts of the paper, developed the CONCOCT module for the platform..
Joseph H Vineis contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Mitchell L Sogin contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Tom O Delmont conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding the deposition of related data:
http://merenlab.org/data/
Funding
AME was supported by the G. Unger Vetlesen Foundation. This project was supported by the Frank R. Lillie Research Innovation Award given by the University of Chicago and the Marine Biological Laboratory. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
