Sebastian B.U. Jordi, Isabel Baertschi, Jiaqi Li, Nadia Fasel, Benjamin Misselwitz, Bahtiyar Yilmaz
Long-read sequencing offers unprecedented opportunities for high-resolution bacterial genome reconstruction, yet fragmented bioinformatics workflows hinder biological insights. StrainCascade 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, StrainCascade provides high-resolution comparative genomics of strain diversity, host-microbe interactions, antimicrobial resistance, and mobile genetic element dynamics.