Quality Control

The first step of any sequencing project is to do quality control of your reads and remove (trim) low quality bases from the end of the read. In this exercise, you will work with Illumina data from the Human Microbiome Project that has already been trimmed. We still want to check the quality of reads, though.

In this part of the metagenomics workshop we will learn how to:

• Check the quality of your raw sequencing data
• Perform quality trimming using sickle

The workshop has the following exercises:

• Quality Control with FastQC
  • Retrieving your data
  • FastQC
• Optional: Quality trimming Illumina paired-end reads
  • Running sickle on a paired-end library
  • Run FastQC again
  • Trimming adapter sequence

At least a basic knowledge of how to work with the command line is required otherwise it will be very difficult to follow some of the examples. Have fun!