A system is provided for encoding genomics data for secure storage and processing. In particular, the system may comprise a client and server operating environment that uses a unique encoding algorithm to transform genomics data and/or metadata to produce encoded genomics data and/or metadata. In some embodiments, the encoded genomics data and/or metadata may be encrypted using one or more encryption algorithms. The encoded and/or encrypted genomics data may be stored on a secure server (e.g., a cloud environment) that may perform subsequent processing steps on the encoded and/or encrypted genomics data. Once the processing steps have been completed, the server may transmit one or more outputs associated with the genomics data and/or metadata to a client device. In this way, the system provides an efficient and secure way to store and process genomics data.