Autocycler is a tool for generating consensus long-read assemblies for bacterial genomes. It is the successor to Trycycler, and for most users, I recommend Autocycler over Trycycler.

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

Autocycler does not (yet) have a publication. If you use it in your research, please cite the following:
Wick RR. Autocycler. https://github.com/rrwick/Autocycler. 2025. doi:10.5281/zenodo.14642607.