I am trying to assess the quality of some metagenomic ONT data. I was suggested to use NanoPlot to assess the 'quality' of the data but don't really understand the output. I know the higher the quality score the higher the probability that a particular decision is correct.
However i have two ONT datasets that are identical apart from the type of sequencing kit used. They have different quality score but the one with higher quality score has a lot lower total reads, does this impact the quality score?
E.g. data1 = quality score 11 with 500,000,000 total reads. data2 = quality score 12 with 100,000,000 total reads.
Also could someone explain to me how quality score conveys to percent accuracy. I have seen that a quality score of 10 correlates to a percent identity of 90. How would i work out what a quality score of 12 correlates to?
I also haven't filtered or trimmed the reads before using nanoplot is this something i need to do before using nanoplot?