d-cameron
commented
2 years ago GRIDSS is designed to detect rearrangements from a sample sequenced with short reads against a single reference genome. Is it not designed for assembly-to-assembly rearrangement detection.
These sort of assembly-level comparison are best using one of the comparative genomics tools designed for this purpose.
Hi there, I wonder if it is possible to use gridss to find re-arrangements between two chromosome-level genome assemblies. I would appreciate it if you could guide me.