Sequence Quality Control

Some HIV researchers are convinced that careful lab work is enough to prevent contamination. After seeing many examples of contamination pass by, we disagree. Contamination happens frequently, even in the best laboratories. It is not a thing of the past; cases of contamination can still be found in new publications. Screening for contamination should be done before the analysis of the sequences, and periodically during the course of large sequencing studies, so problems can be detected and corrected early. To show what contamination looks like in practice, we have collected some illustrative examples of (mostly published) datasets where contamination is a problem, and included some references that discuss instances and consequences of contamination. Following the steps below will help to check your sequences. They are no substitute for common sense and precautions, but they may help reveal contamination in your sequences. We have created interactive Web pages