Session 2: Raw data & QC

The second session deals with raw metagenomics data and the quality controls and pre-processing steps we need to do, including:

  • a brief look at different sequencing techniques

  • what can go wrong when sequencing

  • sequencing quality scores

  • quality reports

  • adapter, spike-in, and host genome removal

The recording is available on the University of Amsterdam’s media site. You can find the slides here: slides session 2.

Here’s a link to a nice site showing several important tools for handling .fastq files: Quality Control and preprocessing of short reads