Andrew Jarman
Andrew Jarman
Andrew Jarman
Helios Scholar
School: Arizona State University
Hometown: Mesa, Arizona
Mentored by: Jonathan Keats, Ph.D.

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Automating Quality Control Stat Collection

The current workflow to analyze quality control (QC) results from sequencing and alignment is a manual, time consuming process that many users forego. QC metrics tell the story of the data and how significant the data may, or may not be; this should be one of the first metrics checked upon alignment completion. To automate the process, we  have developed a new automated workflow that will streamline the process, allowing users to retrieve QC results from TGen's laboratory information management system (LIMS) directly with no manual intervention. This will allow QC metrics such as insert size, % mapped, and median 5’ to 3’ bias to be available for all samples with a click of a few buttons.  The repository of the new QC metric collection workflow will be used within TGen’s internal data analysis pipeline. Having QC metrics easily accessible in the LIMS system will allow users to quickly assess sample quality before commencing downstream analyses

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