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microPITA Tutorial

microPITA (microbiomes: Picking Interesting Taxonomic Abundance) is a computational tool enabling sample selection in two-stage (tiered) studies. Using two-stage designs can more efficiently allocate resources, reducing study costs, and maximizing the use of samples.

microPITA is available as a Galaxy module, a Homebrew formula, a Docker image, and included in bioBakery (VM and cloud). For additional information, please refer to the microPITA paper.

We provide support for microPITA users. Please join our Google group designated specifically for microPITA users. Feel free to post any questions on the google group by posting directly or emailing micropita-users@googlegroups.com.



Overview

The following figure shows the workflow for microPITA.

microPITA.png

1. microPITA (Galaxy module)

microPITA requires a PCL or BIOM input file. For further information on details of format, please refer to the microPITA user manual. For the purpose of this tutorial we will be using a sample input file Test.pcl depicting the general format of the input file.

  • Go to the Huttenhower Galaxy Server: http://huttenhower.sph.harvard.edu/galaxy/
  • Click on the Get Data -> Upload File link on the left pane and upload the demo file Test.pcl. You can do this by clicking on the Browse button, selecting the demo file, and then pressing the Start button. Select the format micropita.
https://bitbucket.org/repo/49y6o9/images/3266810747-Screenshot%20from%202017-09-01%2018-41-15.png
  • Click on the microPITA -> Run link on the left pane.
    • Select the input data from the Input file drop-down menu.
    • Specify the last metadata row in the sample, after which the microbial species are listed. For this demo, select Label.
    • Select the sample selection method from the Select method drop-down menu. For this demo, select representative.
    • Click on Execute
https://bitbucket.org/repo/49y6o9/images/3783979542-Screenshot%20from%202017-09-05%2018-40-14.png

The results will appear on the right pane. You may proceed with viewing it (by clicking on the Eye symbol) or downloading it on your computer (by clicking on the Save symbol). The output file will depict the samples that are representative of the survey.


2. microPITA (Homebrew/Docker/VM)

microPITA can be installed with Homebrew or run from a Docker image. Please note, if you are using bioBakery (Vagrant VM or cloud) you do not need to install microPITA because the tool and its dependencies are already installed.

Install with Homebrew: $ brew install biobakery/biobakery/micropita

Install with Docker: $ docker run -it biobakery/micropita bash

If you would like to install from source, refer to the microPITA user manual for the dependencies and installation instructions.

To run MicroPITA:

  • Open a terminal and create an input folder.
  • Place the sample input file in the input folder, and run the following command:
$ MicroPITA.py --lastmeta Label -m representative input/Test.pcl output.txt

This will generate an output.txt file containing the results.

For further analysis options and more information, please refer to the detailed documentation.


Notes

Please visit http://huttenhower.sph.harvard.edu/micropita for more information

Updated