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:

• version v0.1.3 - the corresponding version of this page.
• version v0.2.0 - the corresponding version of this page.
• version v0.2.1 - the corresponding version of this page