ABSTRACT. Large-scale next-generation sequencing (NGS)-based resequencing detects sequence variations, constructs evolutionary histories, and identifies phenotype-related genotypes. However, NGSbased resequencing studies generate extraordinarily large amounts of data, making computations difficult. Effective use and analysis of these data for NGS-based resequencing studies remains a difficult task for individual researchers. Here, we introduce ReSeqTools, a full-featured toolkit for NGS (Illumina sequencing)-based resequencing analysis, which processes raw data, interprets mapping results, and identifies and annotates sequence variations. ReSeqTools provides abundant scalable functions for routine resequencing analysis in different modules to facilitate customization of the analysis pipeline. ReSeqTools is designed to use compressed data files as input or output to save storage space and facilitates faster and more computationally efficient large-scale resequencing studies in a user-friendly manner. It offers abundant practical functions and generates useful statistics during the analysis pipeline, which significantly simplifies resequencing analysis. Its integrated algorithms and abundant sub-functions provide a solid foundation for special demands in resequencing projects. Users can combine these functions to construct their own pipelines for other purposes.

Purpose: The current status quo of QA data management consists of a mixture of paper‐based forms and spreadsheets for recording the results of daily, monthly, and yearly QA tests for both CT scanners and LINACs. Unfortunately, such systems suffer from a host of problems as, (1) records can be easily lost or destroyed, (2) data is difficult to access — one must physically hunt down records, (3) poor or no means of historical data analysis, and (4) no remote monitoring of machine performance off‐site. To address these issues, a cloud based QA data management system was developed and implemented. Methods: A responsive tablet interface that optimizes clinic workflow with an easy‐to‐navigate interface accessible from any web browser was implemented in HTML/javascript/CSS to allow user mobility when entering QA data. Automated image QA was performed using a phantom QA kit developed in Python that is applicable to any phantom and is currently being used with the Gammex ACR, Las Vegas, Leeds, and Catphan phantoms for performing automated CT, MV, kV, and CBCT QAs, respectively. A Python based resource management system was used to distribute and manage intensive CPU tasks such as QA phantom image analysis or LaTeX‐to‐PDF QA report generation to independent process threads or different servers such that website performance is not affected. Results: To date the cloud QA system has performed approximately 185 QA procedures. Approximately 200 QA parameters are being actively tracked by the system on a monthly basis. Electronic access to historical QA parameter information was successful in proactively identifying a Linac CBCT scanner's performance degradation. Conclusion: A fully comprehensive cloud based QA data management system was successfully implemented for the first time. Potential machine performance issues were proactively identified that would have been otherwise missed by a paper or spreadsheet based QA system.