Illumina QC analysis

Basic quality-control monitoring of Illumina FastQ sequence data.

Sequencing QC is a quality control to ensure that the raw data is of good quality and that there are no problems or biases in your data. To achieve this end we use a number of tools, for example CheckQCFastQC and FastQ Screen. This allows us to check the general quality of the generated data, and screen for potential contaminants.


CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria -


This is a Nextflow pipeline for generating sequencing reports for the SNP&Seq Technology platform, NGI Uppsala, SciLifelab Genomics.

When we run analysis

We run this analysis routinely for all projects.
The analysis works with any species.

Last Updated: 22nd March 2023