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 CheckQC, FastQC and FastQ Screen. This allows us to check the general quality of the generated data, and screen for potential contaminants.
The results of the QC analysis will be summarized in a Multiqc report and provided as part of the data delivery.
NationalGenomicsInfrastructure/ngi_pipeline
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Code driving the production pipeline at SciLifeLab
Molmed/checkQC
https:
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria - http://checkqc.readthedocs.io/
Molmed/seqreports
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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: 27th March 2026