Read-through adapters can appear at the ends of sequencing reads

Many sequencing platforms require the addition of specific adapter sequences to the end of the fragments to be sequenced. For an individual fragment, if the length of the sequencing read is longer than the fragment to be sequenced then the read will continue into the adapter sequence on the end. Unless it is removed this adapter sequence will cause problems for downstream mapping, assembly or other analysis.

February 7, 2016 Cutadapt, FastQC, Skewer, Trim Galore!