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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Query about "Input data metrics" section in log file #210

Closed daniellesloan closed 1 year ago

daniellesloan commented 1 year ago

Hi, I was hoping you could provide clarity on "Input data metrics" section within the log file. I have ran NOVOPlasty twice using the same seed and read data but changed the k-mer size. As you can see from the attached images, the "Input data metrics" section for the k-mer 33 assembly lists 3 values whilst the section for the k-mer 55 assembly lists 5 values, including "Organelle genome %" and "Average organelle coverage". What do these two values mean, and does this mean that there is no mitogenome organelle assembled by the k-mer 33 run? k-mer33_log_screenshot k-mer53_log_screenshot

ndierckx commented 1 year ago

it only gives these two metrics when it was able to circularize the assembly. The 33 is maybe missing a small part, so it didn't circularize.. the % is an estimation of the fraction of mitoreads in the dataset, and the other one is the sequencing depth.. Seems very high in your case