MIRA 3.4 can be run in three ways: mapped with a reference/backbone sequence, de novo with no reference, and de novo with the optional reference. I’m looking for an explanation of how the process differs in each case, since the output assembly sequences are all different. Especially how de novo with the mapping reference is performed, since it seems to perform the best but it’s unclear if it is truly de novo or reference-guided.
Welcome, @ctber
The definitive guide would be the publications associated with the tool. Scroll down to the bottom of tool forms to find the Help section. You’ll find quick help (these are the parts that the authors thought were worth pulling out), plus Citations that include publications and other author resources when available.
Those links point to the underlying algorithm documentation here → MIRA / Wiki / Home
Hope this helps! 