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bioRxiv · 10.64898/2026.02.04.698786

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

Jordi, S. B. U.·Baertschi, I.·Li, J.·Fasel, N.·Misselwitz, B.·Yilmaz, B.
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Abstract

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.

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Jordi, S. B. U., Baertschi, I., Li, J., Fasel, N., Misselwitz, B., Yilmaz, B.. 2026-02-06. StrainCascade: An automated, modular workflow for high-throughput long-read bacterial genome reconstruction and characterization. https://doi.org/10.64898/2026.02.04.698786

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