I have 3 strains of bacteria, one wildtype and 2 mutants derived from the wildtype. I sequenced all 3 genomes with MiSeq 2x300bp. All of the genomes are still in contigs. I would like to align these contigs to see if some overlap in an attempt to fill in gaps and make a more complete genome or at least to see if the mutants have any large deletions. Does anyone know of a program that can do this kind of alignment?
(PS. I know this won't work if it ends up being that the mutants are severely different than the wildtype, but I think they should be fairly similar, i.e. just point mutations)
Thank you in advance!