Plasmids are DNA molecules in the cytoplasm of organisms such as bacteria, yeast or filamentous fungi, free from the nuclear genome (or chromosome). Plasmids can replicate autonomously, maintain a constant copy number in the progeny cells and express genetic information. Plasmids are commonly used as vectors in genetic engineering and are available in linear and circular forms.

Plasmid sequencing is the process of determining the sequence of a plasmid. According to "Bacterial strains for the production and testing of biological products" in Pharmacopoeia of the People’s Republic of China (2020), exogenous genes and host genes should be tested. The determination of plasmid sequence in genetically engineered bacteria can clarify the base composition of the plasmid sequence and determine the insertion position of the target gene. Plasmid sequencing can be realized by high-throughput sequencing analysis technology, which provides a solution for the quality management of bacterial strains used for production in the pharmaceutical field.