I am writing a program in Python that uses BWA aligner to map reads to a reference plasmid genome which then outputs a consensus file and aligned against the reference genome using Clustal Omega. I would like to output an easy to visualise graphic of the alignment that is similar to the bottom alignment map in Benchling (figure 2 & 3 in the link attached as an example).
I have checked on Benchling's GitHub and their source code to see if they are using an existing open source program to create these visuals or they have created their own program to do so but can't seem to find where this graphic is coming from. I haven't had much experience working with creating graphics so if any one has a few ideas of how to go about creating a graphic that is similar to this I would appreciate some guidance. I have looked into using Tkinter and PIL but not quite sure how to go about using them as the sequences are between 8000-12000 bp's long and I am not sure that colouring each individual pixel depending on if it matches the reference is the best course of action as I think that would make the image quite lengthy.