Keanu: a novel visualization tool to explore biodiversity in metagenomes

• Published in: BMC bioinformatics Vol. 20; no. Suppl 2; pp. 103 - 149
• Main Authors: Thrash, Adam, Arick, Mark, Barbato, Robyn A., Jones, Robert M., Douglas, Thomas A., Esdale, Julie, Perkins, Edward J., Garcia-Reyero, Natàlia
• Format: Journal Article
• Language: English
• Published: London BioMed Central 14.03.2019; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Abundance; Alaska; Algorithms; Biodiversity; Bioinformatics; Biomedical and Life Sciences; Classification; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Data analysis; Data processing; Datasets; Genetic aspects; Genetic research; Genomes; Genomics; Holocene; Information visualization; Life Sciences; Metagenomics; Metagenomics - methods; Methods; Microarrays; Paleosols; Researchers; Shotgun sequencing; Shotguns; Software; Taxonomy; Visualization; Visualization tool; Websites; United States; United States > US; Alaska; Metagenomics; Alaska; Holocene; Shotgun sequencing; Visualization tool
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2629-4

Background 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. Results 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. Conclusions 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 .