StaticSection Trimming

Input paired-end reads are merged according to orientation and trimmed with Trimmomatic version 0.36. In particular, Trimmomatic is called in paired-end mode (PE) with added parameters applied in the order they are specified:

ILLUMINACLIP:<path>/TruSeq3-PE.fa:2:15:4:1:true MINLEN:20

• ILLUMINACLIP trims adapter sequences specified by TruSeq3-PE.fa
  • 2 (seedMismatches) is a maximum mismatch count for full matches.
  • 15 (palindromeClipThreshold) indicates the quality of match required for palindrome read alignment. The palindrome mode identifies adapter read-through by comparing the forward and reverse reads.
  • 4 (simpleClipThreshold) indicates the accuracy a match between an adapter and read must have.
  • 1 (minAdapterLength) indicates minimum adapter length for palindrome mode. This value is minimized to optimize adapter detection, leveraging a low false positive rate for palindrome mode.
  • true (keepBothReads) indicates that both reads should be kept when an adapter is trimmed in palindrome mode.
• MINLEN:20 removes reads which are less than 20 bases (performed after all other trimming is completed).

To learn more about these settings, refer to the Trimmomatic documentation.