Mason Lab - Pathomap / Ancestry Mapper (Public)

Part of the Pathomap Project developed by the Mason Lab at Weill Cornell Medical College.

Input VCF files and output Admixture and Pathomap Plots to determine the ancestry of individual humans!

In order to run this pipeline, you can create a free account on the Curoverse home page. Then follow the instructions in the tutorial to use the test data or input your own data!
This tutorial demonstrates how to run the Ancestry Mapper pipeline using the example that the Mason Lab provides at their page. PathoMap is a research project by Weill Cornell Medical College to study the microbiome and metagenome of the built environment of NYC. The Pathomap publication is available here: Afshinnekoo et al., Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics, Cell Systems 2015.

  • Start at the Curoverse website and click Log In at the top. We currently support all Google / Google Apps accounts for authentication. By simply choosing a Google-based account, your account will be automatically created and redirect to the Arvados Workbench.
  • In the top right corner, click on the Run a pipeline… button. Doing so opens a dialog box titled Choose a pipeline to run.
  • Select Mason Lab — Ancestry Mapper (public) and click the Next: choose inputs button. Doing so loads a new page to supply the inputs for the pipeline.
  • The default inputs from the Ancestry Mapper source code repository are already pre-loaded. Click on the Run button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
  • After the pipeline starts running, you can track its progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label under the job the column when the pipeline completes successfully. The current run time of the job in CPU and clock hours is also displayed. You can view individual job details by clicking on the job name.
  • Once the job is finished, the output can be viewed to the right of the run time.
  • Click on the download button to the right of the file to download your results, or the magnifying glass to quickly view your results.