Methods and control compositions for sequencing

A method for monitoring cross-contamination or sample swapping over all steps of a DNA sequencing protocol including collection of a sample comprising DNA, DNA extraction from the sample, purification of the extracted DNA, library preparation, and sequencing, the method comprising,

• a) spiking a first sample with a control composition comprising a first nucleic acid construct wherein the first nucleic acid construct comprises at least one barcode sequence fragment linked to at least one universal sequence fragment and wherein the first nucleic acid construct is a deoxyribonucleic acid construct;
• and then
• b) extracting total DNA wherein total DNA comprises the DNA from the first sample and DNA from the first nucleic acid construct;
• c) purifying total DNA;
• d) preparing a library from total DNA;
• e) sequencing the extracted, purified total DNA;
• f) detecting the first nucleic acid construct in total DNA;
• wherein a different second nucleic acid construct with a different barcode sequence fragment linked to at least one universal sequence fragment is spiked into a second sample and steps b) to e) are then performed for the second sample and wherein detection of the different barcode sequence fragments in the first sample and the second sample is used to determine if cross-contamination between the first sample and the second sample or sample swapping between the first sample and the second sample occurred during sample preparation or processing, and
• g) comparing the extraction efficiency of the first nucleic acid construct and the second nucleic acid construct with the extraction efficiency of the DNA in the first sample and the second sample to control for extraction efficiency wherein the first nucleic acid construct and the second nucleic acid construct are encapsulated, before spiking the first nucleic acid construct and the second nucleic acid construct into the first sample and the second sample, in a simulated cell membrane that mimics the cell membrane of the prokaryotic or eukaryotic cells in the first sample and the second sample to control for extraction efficiency.