I have two fasta files corresponding to two close genomes (same species, and very close strains). However, the issue is that one of these genome is very fragmented and contains a lot of contigs (346 contigs) which makes the comparison very difficult. Ideally, I would like to find unique regions within the reference genome when compared to the fragmented one.
Most of the time, I use Mugsy to align genomes but in this case, the fragmented genome prevent this tool from performing a complete alignment. I also tried with Mauve or GSAlign but I can not identify unique genomic region on the reference genome.
Do you have any other solutions I could try to solve this, please ?