Detecting Inversions from Genome Alignments

Question

[saamhasan55]

Hello, I have whole genome pairwise alignments generated using Nucmer. The alignment is a table file with chromosome number, starting and end positions of all alignments between the 2 genomes (both for the reference and the query genome). Is it possible to identify inversions between the two genomes from this data?

Thanks

[arnstrm]

Have you tried MUM&Co 1?

[saamhasan55]

No I haven't. But I had a look and it seems quite useful. Just one thing though, would it be suitable for detecting structural variants when comparing different species (as in the genomes in the alignment come from different species)?

Answer 1

[colindaven]

If query and reference genomes are close enough (eg chromosomes are homologous), I would recommend using a dotplot tool for this. They're numerous, fast, and allow the eye to detect patterns which might be inversions.

Another option is to use the old mummerplot to visualize the nucmer alignments nucmer and promer plots generated via mummerplot look identical?

[saamhasan55]

The species diverged around 11 million years ago. They have different karyotypes as well, one is 12 chromosomes, the other 18. Although there is good preservation of synteny between them. Would a dotplot still be a viable option?