🦆🦆 Don't duck that QC thingy 🦆🦆
NOTE: In a past life, QuaC used a different remote Git management provider, UAB Gitlab. It was migrated to Github in Jan 2023, and the Gitlab version has been archived.
QuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES samples and then summarizes their results using pre-defined, configurable QC thresholds.
In summary, QuaC performs the following:
- Runs several QC tools using
BAMandVCFfiles as input. At our center CGDS, these files are produced as part of the small variant caller pipeline. - Using QuaC-Watch tool, it performs QC checkup based on the expected thresholds for certain QC metrics and summarizes the results for easier human consumption
- Aggregates QC output as well as QuaC-Watch output using MulitQC, both at the sample level and project level.
- Optionally, above mentioned QuaC-Watch and QC aggregation steps can accept pre-run results from few QC tools (fastqc,
fastq-screen, picard's markduplicates) when run with flag
--include_prior_qc.
NOTE: QuaC is built to use with Human WGS/WES data. If you would like to use it with non-human data, please modify the pipeline as needed -- especially the thresholds used in QuaC-Watch configs.
Full documentation, including installation and how to run QuaC, is available at https://quac.readthedocs.io.
If you use QuaC, please cite:
Gajapathy et al., (2023). QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data. Journal of Open Source Software, 8(90), 5313, https://doi.org/10.21105/joss.05313
- Manavalan Gajapathy
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