Develop an interactive application to facilitate informed sequencing quality control decisions for downstream analysis on many samples

There's the saying of "garbage in, garbage out" in computer science where the quality of your input influences downstream analyses. Genome sequencing has decreased in cost and so experiments can have many more samples. Manually checking each sample can be time consuming, and less precise. So I propose the development of web application or tool where you can drop in your samples and interactively explore the quality of your samples. This tool could be built by various means. One option would be to develop a Shiny R application, which would require knowledge of R, the Shiny package, and possibly HTML/CSS/JavaScript. Another would be to rely on web development standards (HTML/CSS/JS) to build something like an Electron application for cross browser compatibility and be user friendly. This idea stems from my experience dealing with 16S rRNA sequencing samples. I had a single experiment collect about 200 samples, with a total of about 400 samples for paired end sequencing. Manually viewing all 400 samples is time consuming. Additionally, further analysis of sequencing reads typically require some trimming based on the quality diminishing with longer reads. This tool could also be designed to recommend an ideal trim length based on your specifications of a hard threshold trimming all samples this length, or a dynamic threshold per sample basis. This trimming parameter will depend on the downstream tools used if they can handle such varying read lengths.

Team Lead: Eric Leung | [email protected] | @erictleung | Grad Student | Oregon Health & Science University, USA |