I de novo assembled two microbial strains of the same species into four contigs each. I assume they will be very similar in sequence, but I would like to know if there are SNPs or Indels.
I tried both mummer and Last to align the two genomes and I was able to generate dot plots, but they are mostly useful to give me an overview of the alignment.
I tried loading the maf file that Last produced into Geneious, but that did not work. Converting the MAF file to VCF (which Geneious would be able to open) also doesn't seem trivial.
Can you recommend a tool that lets me visualize differences on a SNP/Indel level?
Any suggestions are appreciated!