Polypolish is a tool for polishing genome assemblies with short reads. Unlike other polishers, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Polypolish is also a conservative polisher, so it is very unlikely to introduce new errors during polishing.

For installation instructions, usage, deeper explanations and more, head over to the Polypolish wiki!

This is the original paper describing Polypolish:
Wick RR, Holt KE. Polypolish: short-read polishing of long-read bacterial genome assemblies. PLOS Computational Biology. 2022. doi:10.1371/journal.pcbi.1009802.

And this is a follow-up paper that describes Polypolish v0.6.0:
Bouras G, Judd LM, Edwards RA, Vreugde S, Stinear TP, Wick RR. How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. Microbial Genomics. 2024. doi:10.1099/mgen.0.001254.