Method and apparatus for compact representation of bioinformatics data

A computer-implemented method for the compression of genome sequence data produced by a sequencing machine, said genome sequence data comprising reads of sequences of nucleotides,

• said method comprising the steps of:
• aligning said reads to one or more reference sequences thereby creating aligned reads,
• classifying said aligned reads according to whether a perfect mapping with said one or more reference sequences is found, the number of mismatches with said one or more reference sequences, the presence of substitutions of symbols, the presence of insertions or deletions or clipped symbols in said aligned reads with respect to said one or more reference sequences, the presence of unmapped reads, thereby creating classes of aligned reads, and
• encoding said classified and aligned reads as a multiplicity of layers of syntax elements comprising descriptors which univocally represent said classified and aligned reads,
• wherein encoding said classified aligned reads as a multiplicity of layers of syntax elements comprises selecting said syntax elements according to said classes of aligned reads,
• wherein the encoding of said classified aligned reads as a multiplicity of layers of syntax elements is adapted according to the statistical properties of the data carried by the layer,
• wherein the encoding of said classified aligned reads as a multiplicity of layers of syntax elements associates a specific source model and a specific entropy coder to each layer,
• wherein there is decomposition of the sequence read data and metadata into homogeneous layers of syntax elements in order to obtain distinct information sources with reduced information entropy.