CheckQC - Quick quality control of Illumina sequencing runs

CheckQC is a program designed to check a set of quality criteria against an Illumina runfolder.

This is useful as part of a pipeline, where one needs to evaluate a set of quality criteria after demultiplexing. CheckQC is fast, and should finish a few seconds. It will warn if there are problems breaching warning criteria, and will emit a non-zero exit status if it finds any errors, thus making it easy to stop further processing if the run that is being evaluated needs troubleshooting.

CheckQC has been designed to be modular, and exactly which “qc handlers” are executed with which parameters for a specific run type (i.e. machine type and run length) is determined by a configuration file.

Instrument types supported in checkQC are the following:

HiSeqX
HiSeq2500
MiSeq
NovaSeq

Contributors

Johan Dahlberg

Matilda Åslin

monikaBrandt

Licence

GPL v3

See the code for CheckQC here: https://github.com/Molmed/checkQC