The first thing to do after data import is to check the quality of the sequencing reads and perform the necessary trimming. This applies no matter whether you are working with Whole Genome Sequencing, Whole Exome Sequencing, Targeted Amplicon Sequencing or Whole Transcriptome Sequencing. In the toolbox there are two different ready-to-use workflows for data preparation, but the Prepare Raw Data ready-to-use workflow is universal and should be used for all applications.
One important part of the preparation of raw data is adapter trimming. To be able to trim off the adaptors, an adapter trim list is required. To obtain this file you will have to get in contact with the sequencing technology vendor and ask them to send this adapter trim list file to you. To learn how to create an adapter trim list, see Trim adapter list.