Solution

Goals

• • Genome skim preprocessing

  • Phylogenetic placement via Skmer/APPLES workflow

  • Customized phylogenetic tree visualization

  • Asynchronous email output

Experimental Design

Our workflow utilizes combinations of published algorithm tools, output parsers, and our own scripts.

• • The published algorithm tools include BBTools, Skmer, APPLES, CONSULT, RESPECT, and FastMe.

    • BBTools contains a suite of tools that we adopted for fastq preprocessing.

    • Skmer computes genetic distances between a query and references.

    • APPLES optimizes query phylogenetic placement from the Skmer output.

    • CONSULT is used to remove contaminate reads from the query.

    • RESPECT is used to estimate genomic parameters like repeat structure.

    • FastMe is a tool that we used for calculating phylogeny tree backbones through inference from the Skmer distance matrix output.

  • We use parsers to manipulate output and prepare data for the next step.

  • We made a Python script to create our final tool which returns a PNG image showing the phylogenetic placement of the query organism among the reference organisms, shown below.

Platform Design Choice

• We contemplated a number of different platforms to build our workflow on, but ultimately decided on Galaxy.

  • Galaxy offers many positives, such as the ability to download output from any intermediate step of the pipeline, customization of the pipeline components, and a well-documented path to tool development.