Gene is the genetic material basis. All life phenomena, like disease and death, are related to Gene. Gene sequencing is a way to read life. With the development of new generation high-throughput sequencing technology, TB or more sequence data will be generated daily. It’s more difficult to interpret these big and complex data than to acquire them. Sequence data interpretation is a critical step in current biological research and has great practical significance. It’s a great challenge for current computer systems and computing models to store, process and analysis massive high throughput sequence data. With survey, especially from BGI (Beijing Genome Institute), the current status, problems and measures taken to process high throughput sequence data will be discussed. However, the challenge is too big to be solved unless more people in different fields work together in depth for a long term.