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 FastQC and FastQ Screen. This allows us to check the general quality of the generated data, and screen for potential contaminants.

Molmed/checkQC

https://github.com/Molmed/checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria - http://checkqc.readthedocs.io/

Molmed/seqreports

https://github.com/Molmed/seqreports

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.