I'm pretty new to the field of bioinformatics so, in advance, I apologize for the silly questions that I'll probably make xD
My task is to assemble the chloroplast genome of purple maize. To do that, I'm using the really helpful NOVOPlasty assembler :D
The assembler has given me a few options as possible assemblies for my chloroplast genome and to discard some of these options, the author recommends me to look at the orientation of particular fragments of the genome (the inverted repeats) of the possible assemblies and exclude the ones that aren't in the correct orientation.
I'd like to know which tools I can use to do this. I was using Mauve and this is what I got: https://imggmi.com/full/2019/6/26/5bbd52d4b1d9d4582b568b6c1e1ee2c8-full.jpg.html
I'll be glad to receive any input :)
Thank you a lot in advance!