About Me:
I am Tra-Vaughn James, a Junior Computer Science major at Earlham College, My interests include cybersecurity, Bioinformatics, and Software Engineering.
Abstract
Bioinformatics is an interdisciplinary field between biology, computer science and statistics, in which software is able to augment, and analyze biological data. To convert this data into useful information the use of various tools, parameters, and dynamically changing reference data is required . As a result, workflow management system such as Shakemake and WDL were created to develop workflows that are scalable, repeatable and shareable. Such tools have become pivotal within large-scale labs, saving bioinformaticians time, resources and streamlining the analysis process. Bioinformatic genomics labs, specifically those involved in ancient DNA, also use a variety of tools and programs toward assessing and producing readable data. However, the scripts that pipeline and assemble such workflows are often not efficiently written. Moreover, there are slight discrepancies in the tools that particular labs use, differing from one to the other, this makes it more difficult to share and scale workflows from other labs. I propose constructing a modular WDL pipeline that will increase both the efficiency and usability, and share-ability of current ancient DNA workflows.
Git Lab Project
https://code.cs.earlham.edu/tjames19/ancient-dna-wdl-workflow/-/tree/master
Research Poster
