Is there any way to use ABACAS for this without concatenating the reference genome into a single FASTA file? I was going to use ABACAS for this awhile back but it just got too messy dealing with the huge, unwieldy concatenated output.

Thanks, ABACAS did a good job.

In my case we are just resequencing a bacterial genome that had already been sequenced some years ago. So, the difference between our sequences is less than 1%.

I would think that ABACAS does not perform well on more distant or complex genomes.

Four our puropose it was good enough.

Best

Christian