In this tutorial, we will work with a dataset of Illumina sequence reads which map to a single gene in the Escherichia coli genome. In this exercise we will prepare the data for mapping by trimming the poor quality bases.
Most next-generation sequencing platforms such as Illumina, Solid, Ion torrent and 454 provide the option of paired-end sequencing, those reads need to be paired (see Overview). In this tutorial, this step has already been done and you are provided with one file of paired reads, with an insert size of 500 bp. Select this file, and you'll see that each sequence is tagged with a forward or reverse tag.
Select the paired list, go to menu Annotate & Predict → Trim using BBDuk. Set to Trim adapters, set to Trim low quality, set Minimum Quality to 20, set to Trim Adapters based on paired read overhangs, with minimum overlap of 20. Finally check Discard Short Reads, with minimum length 20.
The BBDuk trim operation will output a new paired list called yghJ paired Illumina reads (trimmed).