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 paper:
Wick RR, Howden BP, Stinear TP (2025). Autocycler: long-read consensus assembly for bacterial genomes. Bioinformatics. doi:10.1093/bioinformatics/btaf474.