Keanu: a novel visualization tool to explore biodiversity in metagenomes

BMC Bioinformatics

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[1] 0000 0001 0637 9574, grid.417553.1, US Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA;0000 0001 0816 8287, grid.260120.7, Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS, USA;0000 0001 0816 8287, grid.260120.7, Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS, USA;0000 0001 0637 9574, grid.417553.1, US Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA;0000 0004 1098 7777, grid.270913.e, US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Fort Wainwright, AK, USA;0000 0004 1098 7777, grid.270913.e, US Army Engineer Research and Development Center, Cold Regions Research and Engineering Laboratory, Hanover, NH, USA;0000 0004 1936 8083, grid.47894.36, Center for the Environmental Management of Military Lands, Colorado State University, Fort Collins, CO, USA;

关键词: Metagenomics;    Visualization tool;    Holocene;    Alaska;    Shotgun sequencing;   

DOI  :  10.1186/s12859-019-2629-4

来源: publisher

【 摘 要 】

BackgroundOne 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.ResultsKeanu, 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.ConclusionsKeanu 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.

【 授权许可】

CC BY