I used ABACAS to order contigs from my draft assembly (DRAFT). The output fasta file has all 30+ chromosomes glued as one sequence with contigs separated by Ns. This to be expected, since ABACAS demands single fasta reference sequence (REF), so it has no idea about chromosomal ends. While such pseudomolecule is still usable, I want to chop it into individual chromosomes/mitochondrion.
One idea is to blast both chromosomal ends from REF against DRAFT, but if DRAFT's chromosomal ends stick out it will get more complicated than simply taking blat hits ends.
Other is to start with doctored REF sequence where individual fasta headers are replaced by i.e. 11111 Ns to make sure no gaps of this size will be present, rerun ABACAS, then chop at gaps with 11111Ns.
Any other ideas, preferably already tested?