Investigators working in population genomics face large computational challenges in the course of analyzing their data. The goal of the proposed work is to reduce the bioinformatics overhead in conducting population genomic analyses. We are building a pipeline platform to ease the development and implementation of complex population genomic analysis workflows. This will be a browser-based open-source project that will be hosted on a server at Temple University and available for download and local installation. Users will be able to filter their data, conduct both summary-statistic based analyses and in-depth model-based analyses, visualize results, record and reproduce all steps in the analyses, upload those steps to repositories, and interact with developers and other users of the platform.
AIM 1: Develop scripts for: (1) genomic data formatting, filtering, and parsing; (2) execution, control; (3) real-time monitoring long-running analyses; and (4) mining and visualization of results.
AIM 2: Incorporate the scripts into a graphical user interface (GUI) as part of the Galaxy Project (www.galaxyproject.org).
AIM 3: Add additional tools for data processing (phasing, imputation), convergence assessment for model-based methods, ABBA-BABA and selection scans, more advanced tools for visualizing results, and mixture model-based analyses of demography and migration.