A pipeline used to detect structural variants between two de novo assemblies of Lake Whitefish (dwarf vs. normal)
For now, this is really a collection of scripts that have been used. Each number tend to correspond to one method and will take place in a folder with the same number. When some scripts are calle 7a, 7b, 7c, they have been used in this order.
NB: I have not managed to run neither SVMU nor paftools.
Assemblytics output was complex to deal with and this tool start to be slightly older. So we chose to use SVIM-ASM, SYRI and MINIGRAPH-BUBBLE to detect SVs between assemblies.