structural variants in de novo genome assemblies

Question

[Anand Rao]

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!

Answer 1

[WouterDeCoster]

I think mummer is something you could use to align entire genomes with each other: http://mummer.sourceforge.net/ You can generate plots like http://mummer.sourceforge.net/examples/dotplot.gif which will highlight structural variation between your two genomes.

[Anand Rao]

Thanks, but before I go off to read the MUMmer manual, I am curious to know whether the alignments will help me identify and extract out identity, coordinates and sequences of those regions that are variant between pairs of genomes. Would you happen to know? I am sort of interested in genome-wide plots and variation, but I am much more interested in locus level variation across genomes.... In that context, can MUMmer deal with more than 2 genomes at a time (i.e. not just pairwise but multi-genome comparisons) and report PAV and CNV amongst other structural variants?