This study evaluates the effectiveness of short-read polishing tools for improving bacterial genome assemblies generated by Oxford Nanopore Technologies (ONT). The researchers introduce Pypolca (with default and careful parameters) and Polypolish v0.6.0 (with a new careful parameter) and assess their performance across varying short-read depths. They find that most short-read polishers introduce false-positive errors at low depths, except for Polypolish-careful and Pypolca-careful. Polypolish-careful never introduces false-positive errors, while Pypolca-careful is the most effective polisher. The study recommends different polishing strategies based on short-read depth: Polypolish-careful alone for very low depths (<5×), Polypolish-careful and Pypolca-careful for low depths (5–25×), and Polypolish-default and Pypolca-careful for sufficient depths (>25×). The results show that approximately 25× short-read depth is sufficient to polish almost all ONT-only assembly errors. The study also highlights the importance of using conservative polishers in scenarios with low read depth or extreme GC content, and emphasizes the need for careful polishing to avoid introducing errors in bacterial genome assemblies. The findings suggest that short-read polishing is crucial for achieving high-quality bacterial genome assemblies, especially when combined with ONT long-read data. The study provides recommendations for the use of short-read polishing tools in bacterial genome assembly pipelines.This study evaluates the effectiveness of short-read polishing tools for improving bacterial genome assemblies generated by Oxford Nanopore Technologies (ONT). The researchers introduce Pypolca (with default and careful parameters) and Polypolish v0.6.0 (with a new careful parameter) and assess their performance across varying short-read depths. They find that most short-read polishers introduce false-positive errors at low depths, except for Polypolish-careful and Pypolca-careful. Polypolish-careful never introduces false-positive errors, while Pypolca-careful is the most effective polisher. The study recommends different polishing strategies based on short-read depth: Polypolish-careful alone for very low depths (<5×), Polypolish-careful and Pypolca-careful for low depths (5–25×), and Polypolish-default and Pypolca-careful for sufficient depths (>25×). The results show that approximately 25× short-read depth is sufficient to polish almost all ONT-only assembly errors. The study also highlights the importance of using conservative polishers in scenarios with low read depth or extreme GC content, and emphasizes the need for careful polishing to avoid introducing errors in bacterial genome assemblies. The findings suggest that short-read polishing is crucial for achieving high-quality bacterial genome assemblies, especially when combined with ONT long-read data. The study provides recommendations for the use of short-read polishing tools in bacterial genome assembly pipelines.