I have 105 bacterial isolates which are assembled into contigs. I also have a really good, fully assembled, reference genome, consisting of 2 chromosomes.
I would like to align each of my isolates to the reference genome, determine which contigs/sequence belongs to which chromosome and therefore split every fasta sequence into 2 chromosome.
I have been told that mauve is good for this. However, I have 105 isolates and mauve doens't seem to be able to cope with this much data at once. I could align smaller groups to the reference genome at a time. However, is there another way/tool to do this?