Abstract: This invention relates to a gene sequencing quality line data compression pre-processing and decompression and restoration method, and a system, wherein the basic principle of the gene sequencing quality line data compression pre-processing and decompression and restoration is to extract several columns from an inputted quality line document or data block to act as index columns, and then perform rearrangement on all quality line data, all quality lines having a same index column being one group and being arranged together according to their relative positions in the original data block. Since quality line data having a same index column is usually more similar, the data reorganization means can arrange similar gene sequencing data together, so as to increase local similarity of the data.