At the start of every Gencove project, you’ll be required to select the Project Configuration (PC) you’ll want to use (a.k.a pipeline). Our pipelines include a number of automatic quality control (QC) checks to ensure data integrity and quality. Examples of QC checks regularly performed are (1) a check for proper input data formatting; (2) number of bases sequenced; (3) number of bases aligned to the reference genome, and more. If a sample fails any QC check, the sample itself will be marked as failed and no results will be returned besides the input `FASTQ` files.
Depending on the PC being used, there may or may not be additional QC checks performed. The general QC checks/metrics are as follows: