I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline. I would like to compare pair wise (A1 to B1, A2 to B2, A3 to B3 etc) and collect some metrics to see how this two assembly method differs.
I am thinking of doing blastn -query A1 -subject B1, but this created a lot visual alignment, rather than detailed align metrics.
Thank you for your suggestions.