Set Paired Reads
This tutorial provides two unpaired read lists SRR513053 subset F and SRR513053 subset R. Select these two lists and go menu Sequence → Set Paired Reads.
Choose Pairs of documents and then choose Forward/Reverse (inward pointing) with an Expected Distance of 350, confirm Read Technology is set to Illumina Paired End then click OK.
This operation will output a new paired list called SRR513053 subset.
Trim with BBDuk
Select the new paired list, go 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 SRR513053 subset (trimmed).
If you select the trimmed list and scroll through the list you will see that many reads are now trimmed shorter than the original 149 nucleotides. To see the command line output from BBDuk, including list of how many bases and reads have been removed during trimming, click the Info tab above the viewer.
In Exercise 2 we will assemble the trimmed paired reads using the Geneious de novo assembler.
Go to:
Introduction: Introduction
Overview: Overview: Best Practice for preprocessing of NGS reads
Exercise 2: De novo assembly of paired-end data
Summary: Other preprocessing tools and general advice for de novo assembly