Inverted SSC section

[JaviETricas]

Greetings,
I am using the latest version of novowrap from conda. It is a great tool, and I am currently using it to assemble chloroplasts from Hordeum vulgare, but one region appears inverted. Based on its size and position, I have determined that it is the SSC region.
I would like to know if this is a typical failure of novowrap when assembling that section, or if my samples have a part of the chloroplast genome inverted. And if it is something related to novowrap, is there a known way to fix it, or to distinguish whether it is a natural inversion of the plant or not?

Thank you very much in advance for the work of novowrap and the good results obtained with the programme.

[wpwupingwp]

Dear Javi,

novowrap will automatically adjust the orientation of the SCC or LSC region to be same with the given reference. The reference is fetched from NCBI RefSeq database if you did not set the reference genbank file. You can find structure comparision result in .pdf file (if the assembly is finished).

In the paper, we also proved that both orientation is naturaly existed in the plant cell. You can find the details in the supplementay materails.

Ping Wu