Order in trim.seqs


what’s the order of trimming in trim.seqs? Does the quality trimming happen before the length trimming?


Yes, the quality trimming is done before the length is evaluated. The order of trimming is as follows:

  1. Remove Linkers, if provided
  2. Remove Barcodes, if provided
  3. Remove Spacers, if provided
  4. Remove Primers, if provided
  5. Trim to keepfirst and removelast parameters, if provided
  6. Trim based on quality parameters, if provided
  7. Trim length, if provided

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