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 ?
Have you tried reference guided scaffolding of the contigs? You might be able to place them and pad with Ns to get around some of the fragmentation, but you'll still be missing a fair bit of info from those regions I imagine.