Plot assembly coverage?

[jaktykusuma]

Hello,

Many thanks for this amazing software. But I was wondering if you could provide (or suggest) a way to plot the assembly coverage? In the provided log file, I can only have the information on the "Average embplant_pt base-coverage = 41.2".

Thank you for your input.

Best

get_org.log.txt

[Kinggerm]

Yes, there is a script for doing this in GetOrganelle, evaluate_assembly_using_mapping.py, which can circularize the reference and generate the reads mapping plot (refer to Fig 1). You may find the usage with evaluate_assembly_using_mapping.py -h.

There is a related FAQ that you may want to read.