manual of smudgeplot with jellyfish - KamilSJaron/smudgeplot GitHub Wiki
The current version of smudgeplot does not support Jellyfish (or KMC) as k-mer counters. There are some good reasons we decided to do that - the algorithm that extract k-mer pairs is now implemented in C and operates directly on FastK database. It is ~60x faster than previous versions, it is fully parallelised and it uses negligible amounts of memory - it is really much better than anything we had before.
Jellyfish was compatible with previous versions, you can check the older tutorials, but again, I urge you not to use it, use the latest version instead: