Quality control templates ensuring validity of sequencing-based assays

A method for characterization associated with at least one of sequencing library preparation and sequencing, the method comprising:

• generating a set of quality control template (QCT) molecules, each QCT molecule comprising:
• a target-associated region matching a target sequence region of a target molecule;
• and
• a variation region not matching a corresponding region of the target molecule, the variation region comprising an embedded molecular identifier having a randomly selected nucleotide sequence, wherein the embedded molecular identifier identifies the QCT molecule;
• generating a mixture comprising the set of QCT molecules and nucleic acid molecules of a sample;
• co-amplifying the mixture;
• sequencing the co-amplified mixture to generate sequencing data;
• computationally determining a set of QCT sequence read clusters, using the sequencing data, based on a number of distinct variation regions of the set of QCT molecules identified in the sequencing data;
• computationally determining a count of QCT molecules that were in the mixture prior to the co-amplification based on the set of QCT sequence read clusters;
• and
• based on the count of QCT molecules, determining a sequencing related parameter associated with the at least one of the sequencing library preparation and the sequencing.