Jasper, a tool for Microbiome Maps

Microbiome Visualizations

Jasper for macOS, and for Python and R, is a set of tools for creating rich, interactive microbiome maps that let you explore your metagenomic samples like never before. Jasper uses a Hilbert Curve to place genomes on an interactive canvas that can display thousands of genomes at once. The Hilbert Curve placement allows for the clustering of related taxa into Neighborhoods that can quickly show you how abundant a taxonomic group is.

Color is used as a proxy of abundance: areas with no color (white) represent genomes that are not present in the sample, while areas with a lot of color represent genomes that are very abundant.

If you see an area that is of interest, you can just hover your mouse over it, and look at the bottom status bar to see what genome you are hovering over. Click on an interesting area to bring up a detailed view that shows you the specifics of the genome you clicked on. You can then click on the links to find out a lot more about the genome.

You can share your Microbiome Maps by exporting them as high-resolution images, and you can also print them. See the manual & documentation for for details.

Jasper is FREE and designed for macOS, Python, and R. You can install it from the Mac App Store, or from GitHub.

 

Jasper can handle a lot genomes: the Microbiome Map on the right contains data about 44,000 genomes taken from a buccal mucosa sample (profiled using whole-genome sequencing).

 
 

Fun with Hilbert Curves

You can use the software to create Hilbert Curves. You can learn how these space-filling curves are created and how they can be folded without crossing themselves.

 

Hilbert curves have been used in other disciplines. One of their best uses is the XKCD post on the map of the internet.

XKCD’s Map of the Internet. Credit XKCD.

Requirements

The current versions of Jasper require the following:

  • Jasper GUI

    • macOS 10.15 (Catalina) or later.

    • 4 GB or RAM or more.

  • Jasper CLI

    • Python 3.8, or higher.

    • R, 4.2 or higher.

Input

You will need a community abundance profile for metagenomic whole-genome sequencing, or 16S data. See the Manual for a detailed description of the format.

Command-Line Versions

The CLI versions of Jasper make use of 3rd party Python and R libraries. You can view their requirements at the GitHub repository.

The interactive version of Jasper is designed as a GUI app for macOS.
The command-line version is designed as Python and R scripts that can process many samples in batches.