Quality Control Metrics focused on FASTQ format validity

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 possible QC checks/metrics, focused on FASTQ format validity, are as follows: