PUMAA
Program for Unifying Microbiome Analysis Applications
Tutorials for Microbiome Analysis and Visualization
PUMAA Background
Microbiome research is an attractive direction for course-based undergraduate research experiences (CURES), as sample collection is relatively straightforward and the resulting large datasets give students an opportunity to ask a variety of questions and learn bioinformatics skills. A major challenge for the development of these types of CUREs is that microbiome sequence data requires a number of bioinformatic processing steps before it can be analyzed, which not all instructors have familiarity with. In addition, many of the available data analysis tools require programming skills, or at least familiarity with a command line interface, in order to perform data analysis and visualization.
These barriers to entry led us to develop the Program for Unifying Microbiome Analysis Applications (PUMAA) tool, which includes instructional materials to guide instructors and students through the process of analyzing and visualizing microbiome data.
The PUMAA pipeline includes instructions and curricular materials/tutorials for a suite of published and/or publicly available programs for microbiome data visualization and analysis. Each of which are easily accessible to undergraduates without command line experience.
Using the PUMAA pipeline, students can formulate testable hypotheses linking environmental and sample parameters (metadata) to diversity metrics, community composition, and inferred functional profiles. For example, students can use Microsoft Excel pivot tables and Ranacapa[1] to explore the biodiversity of the samples. Then, the Statistical Analysis of Metagenomic Profiles[2] (STAMP) program enables students to perform statistical tests on microbiome community and functional profiles, and aids in teaching lessons on statistical significance and biological relevance, as well as producing publication-quality figures.
References
[1] Kandlikar, G.S., Gold, Z.J., Cowen, M.C., Meyer, R.S., Freise, A.C., Kraft, N.J.B., Moberg-Parker, J., Sprague, J., Kushner, D.J., and Curd, E.E. (2018). ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000Research 7, 1734.
[2] Parks, D.H., Tyson, G.W., Hugenholtz, P., and Beiko, R.G. (2014). STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30, 3123–3124.
The PUMAA tool is described in more detail here (https://doi.org/10.1101/482380), but in brief it combines previously published processes and tools for microbiome research with a set of custom “plug and play” python scripts for processing 16S sequencing data from a variety of sources. The PUMAA tool allows non-bioinformatics experts to input the standard output files from Anacapa, QIIME or inexpensive commercial sequencing providers such as MrDNA-Lab, and format them for downstream tools.
PUMAA Manual and Tutorials for Microbiome Analysis and Visualization
Manual Version 1.2
This manual includes the detailed written tutorials for each analysis module. See individual pages in this website to download example files and view tutorial slides and videos.
