In Circa, we need to give it the names and sizes of the chromosomes to show.

When showing a single genome, the .fai index file is enough, but when showing two genomes, we need to create a reference file that includes the sizes and orientations of the chromosomes in the order we want to show them.

First, let’s index our FASTA files:

The simplest reference file is just the .fai files concatenated together:

The result looks like this, with the first two columns being the names and sizes.

That’s all we need to set up the coordinates for visualization.

Next, we will use this reference file and the alignments from the previous step to make a circos plot in Circa.