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

iScience 2026 Open access

Read full text
Authors: Sebastian B.U. Jordi, Isabel Baertschi, Jiaqi Li, Nadia Fasel, Benjamin Misselwitz, Bahtiyar Yilmaz
DOI: 10.1016/j.isci.2026.116189
Cited by: 1
References: 36

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.

Fields of Study & Subjects

Genomics and Phylogenetic Studies Bacterial Genetics and Biotechnology Bacteriophages and microbial interactions

Publication details

Journal / source
iScience
Publisher
Elsevier BV
Volume
29
Issue
6
Pages
116189–116189
Publication date
1 June 2026
Language
EN