Considerations of Depth, Coverage, and Other Read Quality Metrics
Derek D. N. Smith, Andrea D. Tyler · 2025
This chapter introduces concepts and best practices in quality control and handling of next-generation sequencing reads and interpretation as they relate to coverage, depth, and read quality characteristics. It provides a brief overview of commonly used technologies and platform specific characteristics affecting read quality, discussing the suitability of short and long reads to produce informative and accurate outputs. Sequencing errors can be systematic in nature due to a bias or deficiency associated with a sequencing technology or preparation technique. The chapter provides a brief overview of some of the challenges associated with commonly used sequencing technologies currently in use for research and molecular diagnostics. It serves as a primer on these topics to provide a foundation for the reader to build upon in identifying the appropriate molecular methods and analysis strategies in tackling diagnostic and research challenges addressed by applying microbial molecular methods.