I have two closely related genomes, with all genes annotated,
Ortholog gene pairs were identified from these two genomes, now I want to find how many genes come with large effect structural variations, such as exon deletion, frameshift, premature codons etc.
I have aligned all ortholog gene pairs based on their gene sequence, the alignment can be view in detail to find whether their are exons that could not be aligned properly, however, their are too many gene pairs, It is impossible to view all these alignments.
Are their tools that can find structural variations based on long sequence alignments?
these days, most people used PE reads to find SVs, I could not find tools that can find SVs based on alignment of assembled contigs/scaffolds onto a reference genome.