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  • I'd like some guidance on bbduk.sh parameters for trimming and filtering raw reads that would fit best for meeting the following criterion. I'm dealing with PE 150bp raw reads and bbduk.sh version 38.84

    1) Discard a read pair if either one read contains adapter contamination;
    2) Discard a read pair if more than 10% of bases are uncertain in either one read;
    3) Discard a read pair if the proportion of low quality bases is over 50% in either one read.‚Äč

    From my understanding of the parameters, point 2 could be met by setting maxns=15. I am not sure on what paramters to use for points 1 and 3. Any help would be much appreciated.
    Last edited by brewseeker; 06-22-2023, 06:09 AM.

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    • Hi Brian,
      This question is regarding the parameter "mincovfraction or mcf" which is available in BBDuk but I notice that it is not available in Seal. Am I missing anything or was this a deliberate choice, perhaps due to computational considerations. Is there a way around? I know I could use "minkmerfraction" but I am a bit worried about missing a few corner cases. Any suggestions to accomplish this functionality using Seal would be very helpful.
      Thanks in advance.

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