Fragmented genomes

[jianshu93]

Hi Team,

How do I perform and all verses all alignment for 10 genomes but each genome is fragmented (e.g. 20 fragments) and the order of those fragments are not known (none of them is complete, all are fragmented). example genome attached. The below one:

wfmash x.fa x.fa -X > x.paf

How do I organize the 10 genome so that each fasta record represent a genomes so that I can align them.

Thanks,
Jianshu

genomes.tar.gz