<i>StrainCascade</i>: An automated, modular workflow for high-throughput long-read bacterial genome reconstruction and characterization

Long-read sequencing offers unprecedented opportunities for high-resolution bacterial genome reconstruction, yet fragmented bioinformatics workflows hinder biological insights. <i>StrainCascade</i> addresses this gap by providing a fully automated, modular pipeline that integrates genome assembly, accurate annotation, and comprehensive functional profiling into a single, reproducible framework. By integrating deterministic execution strategies with a systematic resolution of strain-level structural and functional variability, <i>StrainCascade</i> provides high-resolution comparative genomics of strain diversity, host-microbe interactions, antimicrobial resistance, and mobile genetic element dynamics.