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