Keanu: a novel visualization tool to explore biodiversity in metagenomes

One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, es...

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Bibliographic Details
Published in:BMC bioinformatics 2019-03, Vol.20 (Suppl 2), p.103-103, Article 103
Main Authors: Thrash, Adam, Arick, 2nd, Mark, Barbato, Robyn A, Jones, Robert M, Douglas, Thomas A, Esdale, Julie, Perkins, Edward J, Garcia-Reyero, Natàlia
Format: Article
Language:English
Subjects:
Abundance
Alaska
Alpine environments
Biodiversity
Classification
Data analysis
Data processing
Datasets
Genetic aspects
Genetic research
Genomes
Genomics
Holocene
Information visualization
Metagenomics
Metagenomics - methods
Methods
Paleosols
Researchers
Shotgun sequencing
Shotguns
Software
Taxonomy
Visualization
Visualization tool
Websites
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Summary:One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier. Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska. Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-019-2629-4