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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.

2026-02-06 bioinformatics
10.64898/2026.02.04.698786 bioRxiv
Show 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.

Published in iScience · training set

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.