TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles

  1. Varuni Sarwal
  2. Jaqueline Brito
  3. Serghei Mangul
  4. David Koslicki

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Abstract

Metagenomic taxonomic profiling aims to predict the identity and relative abundance of taxa in a given whole genome sequencing metagenomic sample. A recent surge in computational methods that aim to accurately estimate taxonomic profiles, called taxonomic profilers, have motivated community driven efforts to create standardized benchmarking datasets and platforms, standardized taxonomic profile formats, as well as a benchmarking platform to assess tool performance. While this standardization is essential, there is currently a lack of tools to visualize the standardized output of the many existing taxonomic profilers, and benchmarking studies rely on a single value metrics to compare performance of tools and compare to benchmarking datasets. Here we report the development of TAMPA ( Ta xonomic m etagenome p rofiling evalu a tion), a robust and easy-to-use method that allows scientists to easily interpret and interact with taxonomic profiles produced by the many different taxonomic profiler methods beyond the standard metrics used by the scientific community. We demonstrate the unique ability of TAMPA to provide important biological insights into the taxonomic differences between samples otherwise missed by commonly utilized metrics. Additionally, we show that TAMPA can help visualize the output of taxonomic profilers, enabling biologists to effectively choose the most appropriate profiling method to use on their metagenomics data. TAMPA is available on GitHub, Bioconda and Galaxy Toolshed at https://github.com/dkoslicki/TAMPA , and is released under the MIT license.

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  1. GigaScience

    taxonomic

    Reviewer name: Francesco Asnicar (revision 1)

    This reviewer thanks the authors for their revision. However, the quality of the figures and the main goal the authors would like to reach with the tool named TAMPA is noThe main goal of TAMPA is to allow to compare taxonomic profiling tools, but it is evident from the supplementary figures that the software cannot allow such comparison when the taxonomic tree is large enough, as the circles added to the branches become unreadable. This I believe is a major flaw of the tool that aims to do that specifically and for such cases a smarter way that allow comparing taxonomic profilers should be found. For instance, a legend to each figure created by TAMPA should be added to make immediately clear what the colors represent. Also, for such taxonomic trees that the visualization fails in allowing comparing the taxonomic profilers a different and complementary data should be provided, for instance a table listing all branches and the numbers the depicted circles represent. In addition, such table should allow to overcome the limitation of just 3 tools allowed in the comparison.

  2. GigaScience

    computational

    Reviewer name: Alessio Milanese (revision 1)

    Many thanks to the authors for their detailed responses to my comments.The edits have improved the manuscript and I have only few minor comments.COMMENT 1:In Figure 4b I can see that "Tenericutes" and "Planctomycetes" are both in orange, meaning that they bothhave been measured only by mOTUs. But in the main text I read "mOTUs failed to detect theTenericutes group, while MetaPhlAn failed to detect Planctomycetes", which is wrong.COMMENT 2:I would improve the figure legends. In particular, the description of 4b is the same as in 2a and 3a and 1:"The size of the discs represents the total amount of relative abundance at the corresponding clade in theground truth, or the tool prediction if that clade is not in the ground truth. If the tool predictions agree,a disc is colored half orange and half teal. The proportion of teal to orange changes with respect to thedisagreement in the prediction of that clade's relative abundance between the two tools being compared. Highlighted blue text represents clades where the difference between the relative abundances of the prediction and ground truth exceeds 30%".I would suggest to have this description only for figure 1, and then have a shorter description for thefollowing figures.COMMENT 3:The second color is described sometimes as "green" and sometimes as "teal". For clarity, I would suggestusing just one of the two.

  3. GigaScience

    Metagenomic

    Reviewer name: Francesco Asnicar

    The manuscript by Sarwal et al. presents a novel tool for a standardized visualization of metagenomic taxonomic profiler tools, named TAMPA, that also enables a more general assessments of performances of taxonomic profiler tools by providing an extensive of different metrics.It would be interesting to see (if possible) the comparison of three (or more) taxonomic profiles at the same time. The evaluations shown are always binary, but in a real-case scenario where a user would like to evaluate 3 or 4 different taxonomic profiling tools on his community, it would be great to be able to do it.Other than the evaluation on the agreement between two (or more) taxonomic profiling tools, it is not clear how TAMPA can drive improvement over biologically-relevant question. Although it is clear, as the authors stated in the introduction, that different taxonomic profilers (with different parameters settings) can produce very different taxonomic representations, to support this statement it will be important to be able to show, at least one case, where TAMPA can suggest a different taxonomic interpretation of a microbial community that is also biologically relevant.Figures in general appear to be of low-quality and stretched, please consider improving them as they are the main point of TAMPA.

  4. Version published to 10.1101/2022.04.28.489926v1 on bioRxiv