.. _rawQC:

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Session 2: Raw data & QC
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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 <https://video.uva.nl/media/Metagenomics+101+-+2%7C+Raw+data+and+QC+-+public+version/0_fh6gr3cb>`_. You can find the slides here: :download:`slides session 2 <_static/220222_MetagenomicsQC.pdf>`.

Here's a link to a nice site showing several important tools for handling .fastq files: `Quality Control and preprocessing of short reads <http://barcwiki.wi.mit.edu/wiki/SOPs/qc_shortReads>`_