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!
If you use Autocycler in your research, please cite the following preprint:
Wick RR, Howden BP, Stinear TP. Autocycler: long-read consensus assembly for bacterial genomes. bioRxiv. 2025. doi:10.1101/2025.05.12.653612v1.