Interpretation of .fastg file and advice to simplify about getorganelle HOT 2 CLOSED

Hi Allison,

You don't need to do manual completion in this case. This assembly graph is nearly the same to the example we used in our manuscript (see Figure 2).
You have repeats inside the IRs, causing six possible paths. However, only two (.repeat_pattern1.) out of the six paths have identical IRs, and assumed to be biologically possible ones. So you just need to pick /usr/people/astander/11_Plastome/04_GetOrganelle/GetOrganelle_L6EC.out/plant_cp.K115.complete.graph1.1.repeat_pattern1.path_sequence.fasta and /usr/people/astander/11_Plastome/04_GetOrganelle/GetOrganelle_L6EC.out/plant_cp.K115.complete.graph1.2.repeat_pattern1.path_sequence.fasta as your final result.

Best,
Jianjun

from getorganelle.

Hi Jianjun,

Thank you very much for the detailed advice. Much appreciated.

Kind Regards,
Allison

from getorganelle.