In this tutorial I explain how to perform quality control analysis of NGS data using FastQC. FastQC is a tool used for the quality assessment of NGS data. The overall quality of the series readings is assessed based on; Nucleotide distribution, quality score distribution, GC content, degree of sequence ambiguity, PCR (polymerase chain reaction) duplication.

This FastQC report first lists the basic statistics i.e. file type, total number of sequences etc. Then the quality per base sequence shows a graph that summarizes the range of quality values across all bases at each position in the FASTQ -file. . Then, per basic sequence quality score report, you can see if a subset of your sequences have universally low quality values. This is followed by content per base sequence, which shows the proportion of each base position in a file for which each of the four normal DNA bases has been called.

To understand the rest of the FastQC report, watch part 2 of this FastQC report tutorial.

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