Let's say I have two or more complete bacterial genome sequences produced by Sanger sequencing and/or Nanopore/PacBio (no Illumina reads). The bacterial genomes in question are 95-99% identical on the nucleotide level. What would be the best way to align these genomes (with a pair-wise or multiple alignment) and identify:
- Short variants: single and multiple nucleotide variations (SNP/MNP), indels
- Long variants: longer deletions and insertions, inversions, duplications, translocations and so on
I am aware of MUMmer, Mauve and Mugsy, what other programs should I check? Would be great if they could produce a .VCF file as well.