A computer-implemented method for the storage of a representation of genome sequence data in a genomic file format, said genome sequence data comprising reads of sequences of nucleotides, comprising the steps of: - aligning said reads to one or more reference sequences, thereby creating aligned reads; - classifying said aligned reads into classes, wherein said classifying comprises: - classifying one or more of said aligned reads into a first class when said one or more aligned reads match with said one or more reference sequences without any mismatch; - classifying one or more of said aligned reads into a second class when said one or more aligned reads match with said one or more reference sequences with a number of mismatches; - classifying one or more of said aligned reads into a third class when said one or more aligned reads match with said one or more reference sequences with the presence of substitutions of symbols and the presence of insertions or deletions and soft clipped symbols; - classifying one or more of said aligned reads into a fourth class when said one or more aligned reads do not match with said one or more reference sequences, thereby creating classes of aligned reads; - entropy encoding said classified aligned reads as layers, each layer comprising data blocks, each data block comprising descriptors as a vector of syntax data elements of the same type, said descriptors comprising information data related to the position of the read with respect to the reference sequence, wherein the encoding of said classified aligned reads as layers of syntax data elements is adapted according to the statistical properties of the data or metadata carried by the layer; - structuring said layers of data blocks with header information thereby creating successive access units; - creating a master index table, containing one section for each class of aligned reads, comprising the mapping positions on said one or more reference sequences of the first read of each access units of each class of aligned reads; - jointly storing said master index table and said access unit data. - aligning said reads to one or more reference sequences, thereby creating aligned reads; - classifying said aligned reads into classes, wherein said classifying comprises: - classifying one or more of said aligned reads into a first class when said one or more aligned reads match with said one or more reference sequences without any mismatch; - classifying one or more of said aligned reads into a second class when said one or more aligned reads match with said one or more reference sequences with a number of mismatches; - classifying one or more of said aligned reads into a third class when said one or more aligned reads match with said one or more reference sequences with the presence of substitutions of symbols and the presence of insertions or deletions and soft clipped symbols; - classifying one or more of said aligned reads into a fourth class when said one or more aligned reads do not match with said one or more reference sequences, - classifying one or more of said aligned reads into a first class when said one or more aligned reads match with said one or more reference sequences without any mismatch; - classifying one or more of said aligned reads into a second class when said one or more aligned reads match with said one or more reference sequences with a number of mismatches; - classifying one or more of said aligned reads into a third class when said one or more aligned reads match with said one or more reference sequences with the presence of substitutions of symbols and the presence of insertions or deletions and soft clipped symbols; - classifying one or more of said aligned reads into a fourth class when said one or more aligned reads do not match with said one or more reference sequences, - entropy encoding said classified aligned reads as layers, each layer comprising data blocks, each data block comprising descriptors as a vector of syntax data elements of the same type, said descriptors comprising information data related to the position of the read with respect to the reference sequence, - structuring said layers of data blocks with header information thereby creating successive access units; - creating a master index table, containing one section for each class of aligned reads, comprising the mapping positions on said one or more reference sequences of the first read of each access units of each class of aligned reads; - jointly storing said master index table and said access unit data.