Calour: an Interactive, Microbe-Centric Analysis Tool

Zhenjiang Zech Xu, Amnon Amir, Jon Sanders, Qiyun Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Microbiome analyses can be challenging because microbial strains are numerous, and often, confounding factors in the data set are also numerous. Many tools reduce, summarize, and visualize these high-dimensional data to provide insight at the community level. However, they lose the detailed information about each taxon and can be misleading (for example, the well-known horseshoe effect in ordination plots). Thus, multiple methods at different levels of resolution are required to capture the full range of microbial patterns. Here we present Calour, a user-friendly data exploration tool for microbiome analyses. Calour provides a study-centric data model to store and manipulate sample-by-feature tables (with features typically being operational taxonomic units) and their associated metadata. It generates an interactive heatmap, allowing visualization of microbial patterns and exploration using microbial knowledge databases. We demonstrate the use of Calour by exploring publicly available data sets, including the gut and skin microbiota of habitat-switched fire salamander larvae, gut microbiota of Trichuris muris-infected mice, skin microbiota of different human body sites, gut microbiota of various ant species, and a metabolome study of mice exposed to intermittent hypoxia and hypercapnia. In these cases, Calour reveals novel patterns and potential contaminants of subgroups of microbes that are otherwise hard to find. Calour is open source under the Berkeley Software Distribution (BSD) license and available from https://github.com/biocore/ calour.

Original languageEnglish (US)
Article numbere00269-18
JournalmSystems
Volume4
Issue number1
DOIs
StatePublished - Feb 2019
Externally publishedYes

Keywords

  • Analysis
  • Contamination
  • Heatmap
  • Microbiome
  • Visualization

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics
  • Biochemistry
  • Physiology
  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computer Science Applications

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