Frequently Asked Questions

Q: What is the difference between two different trimming methods?

A: In sangeranalyseR, we provide two trimming methods, “M1” (the default) or “M2”, which represents “method 1” or “method 2” respectively. M1 is the modified Mott’s trimming algorithm that can also be found in Phred/Phrap and Biopython. M2 is like trimmomatic’s sliding window method. If you want to set M1 as your trimming method, you need to assign “TrimmingMethod” to “M1” and “M1TrimmingCutoff” as the threshold that you want. Its default value is “0.0001”. In contrast, you can assign “TrimmingMethod” to “M2” if you want to set M2 as your trimming method. “M2CutoffQualityScore” and “M2SlidingWindowSize” are two parameters that control M2 trimming and their default values are “20” and “10” respectively.