What are some tools that can compare 2 or more plant genomes that are de novo assembled in order to detect Structural Variants and Copy Number Variants?
Please note that I do NOT have access to sequencing reads information for these genomes. Only their assembled genomes. These de novo assembled genomes are of different genotypes of the same plant species.
I'd prefer a software that is accessible at the command line and not just via web browser access. Thanks!