Welcome @Bioinfoufgd
Hopefully I can explain a bit about the usage! You’ll need to include some reads files since what this tool is doing is generating statistics about your specific reads versus your assembly.
I created a very simple demonstration history here that you can review or import to play around with to see how it is all organized.
This is a screenshot of the tool form with the inputs from the history selected.
- The assembly in a single file
- The reads are each in their own single file, then they are combined into a paired-end collection folder. The tool is expecting this folder shape and will not accept the read files just as individual datasets.
I’m guessing that you might still need to organize the reads into a paired end collection folder.
Here is a little movie showing how to do it. Let us know if it helps! 