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High-speed scanning is a huge challenge to the motion control of step-scanning gene sequencing stage. The stage should achieve high-precision position stability with minimal settling time for each step. The existing step-scanning scheme usually bases on fixed-step motion control, which has limited means to reduce the time cost of approaching the desired position and keeping high-precision position stability. In this work, we focus on shortening the settling time of stepping motion and propose a novel variable step control method to increase the scanning speed of gene sequencing stage. Specifically, the variable step control stabilizes the stage at any position in a steady-state interval rather than the desired position on each step, so that reduces the settling time. The resulting step-length error is compensated in the next acceleration and deceleration process of stepping to avoid the accumulation of errors. We explicitly described the working process of the step-scanning gene sequencer and designed the PID control structure used in the variable step control for the gene sequencing stage. The simulation was performed to check the performance and stability of the variable step control. Under the conditions of the variable step control where the IMA6000 gene sequencer prototype was evaluated extensively. The experimental results show that the real gene sequencer can step 1.54 mm in 50 ms period, and maintain a high-precision stable state less than 30 nm standard deviation in the following 10 ms period. The proposed method performs well on the gene sequencing stage. [ABSTRACT FROM AUTHOR]