Assessment of Watershed Model Simplification and Potential Application in Small Ungaged Watersheds: A Case Study of Big Creek, Atlanta, GA

Technological and methodological advances of the past few decades have provided hydrologists with advanced and increasingly complex hydrological models. These models improve our ability to simulate hydrological systems, but they also require a lot of detailed input data and, therefore, have a limited applicability in locations with poor data availability. From a case study of Big Creek watershed, a 186.4 km2 urbanizing watershed in Atlanta, GA, for which continuous flow data are available since 1960, this project investigates the relationship between model complexity, data availability and predictive performance in order to provide reliability factors for the use of reduced complexity models in areas with limited data availability, such as small ungaged watersheds in similar environments. My hope is to identify ways to increase model efficiency without sacrificing significant model reliability that will be transferable to ungaged watersheds

A comprehensive benchmarking of WGS-based deletion structural variant callers.

Advances in whole-genome sequencing (WGS) promise to enable the accurate and comprehensive structural variant (SV) discovery. Dissecting SVs from WGS data presents a substantial number of challenges and a plethora of SV detection methods have been developed. Currently, evidence that investigators can use to select appropriate SV detection tools is lacking. In this article, we have evaluated the performance of SV detection tools on mouse and human WGS data using a comprehensive polymerase chain reaction-confirmed gold standard set of SVs and the genome-in-a-bottle variant set, respectively. In contrast to the previous benchmarking studies, our gold standard dataset included a complete set of SVs allowing us to report both precision and sensitivity rates of the SV detection methods. Our study investigates the ability of the methods to detect deletions, thus providing an optimistic estimate of SV detection performance as the SV detection methods that fail to detect deletions are likely to miss more complex SVs. We found that SV detection tools varied widely in their performance, with several methods providing a good balance between sensitivity and precision. Additionally, we have determined the SV callers best suited for low- and ultralow-pass sequencing data as well as for different deletion length categories

Unlocking capacities of genomics for the COVID-19 response and future pandemics

During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing