command-line-interfacebioinformaticssequencing

In Trimmomatic is there any default values for sliding window?


If I give a command for AVGQUAL:20 without sliding window will it set any default values for the slidingwindow?


Solution

  • If you check the trimmmomatic website http://www.usadellab.org/cms/?page=trimmomatic , you will find the manual there.

    In the manual it says for AVGQUAL: AVGQUAL: Drop the read if the average quality is below the specified level

    Therefore no window is needed, as this step sums up all qualities, divides by length and checks whether the threshold is reached or not, and then drops or retains the read.