Abstract: A filter processing method for a sequence alignment is provided. The method includes: searching for absolute locations of all seeds of a to-be-aligned sequence in a reference sequence; performing segmentation on the absolute locations of the seeds to obtain relative locations of the seeds; dividing the reference sequence into multiple reference sub-sequences and establishing a mapping relationship between a relative location of each seed and a corresponding reference sub-sequence; determining a reference sub-sequence to which each seed belongs and counting the occurrence numbers of the seeds in each reference sub-sequence; filtering out a reference sub-sequence that does not meet a preset condition to obtain a target reference sub-sequence; and recovering a real CAL based on a difference between a relative location and an absolute location of each seed in the target reference sub-sequence.