Abstract: The invention relates to a method for encoding of quality values of a data structure, whereby said data structure includes a plurality of continuous fragments, each continuous fragment comprises a sequence of symbols derived from a symbol alphabet and corresponds to a segment of one reference sequence of one or more reference sequences, whereby each continuous fragment is aligned to locus indexes of one of said reference sequence and at least a portion of said continuous fragments overlap at an aligned locus index, and includes, further, a plurality of quality values, each quality value is derived from a quality value alphabet and is assigned to a corresponding symbol of one of the continuous fragments, whereby each quality value indicates a likelihood that the corresponding symbol in the corresponding continuous fragment is correct, wherein the method comprises the steps executable by a data processing system: —determine the quality values at a specific locus index, which are assigned to symbols of continuou

Abstract: Method for encoding of quality values of a data structure, whereby said data structure comprises a set of genomic reads, wherein the method comprises the following steps executable by a data processing system: ascertain the quality values of each read covering a certain index locus, —determine a codebook identifier identifying a specific codebook from a plurality of codebooks for said certain index locus based on the ascertained quality values of said certain index locus, whereby each code-book provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, —quantizing all ascertained quality values at said certain index locus using the specific codebook identified by the codebook identifier at said certain index locus in order to obtain for each quality value at said certain index locus a corresponding quantized quality value, and —encode all determined codebook identifiers using a first entropy encoder and encode all qu

Abstract: Method for encoding of quality values of a data structure, whereby said data structure comprises a set of genomic reads, wherein the method comprises the following steps executable by a data processing system: ascertain the quality values of each read covering a certain index locus, determine a codebook identifier identifying a specific codebook from a plurality of codebooks for said certain index locus based on the ascertained quality values of said certain index locus, whereby each code-book provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, quantizing all ascertained quality values at said certain index locus using the specific codebook identified by the codebook identifier at said certain index locus in order to obtain for each quality value at said certain index locus a corresponding quantized quality value, and encode all determined codebook identifiers using a first entropy encoder and encode all quant

Abstract: The present invention relates to a method for compressing genomic data, whereby the genomic data are stored in at least one data file containing at least a plurality of reads built by a genome sequencing method, whereby each read includes a mapping position, a CIGAR string and an actual sequenced nucleotide sequence as a local part of the donor genome, comprising the steps: —unwind a nucleotide sequence of a current read of one of said data files by using the mapping position and the CIGAR string of said current read, whereby said current read has at least one previous read, —compute a difference between the unwound nucleotide sequence of said current read and an unwound nucleotide sequence of at least one of said previous reads, whereby said difference contains the differences of the mapping positions and the nucleotide sequences, —pass said computed difference to an entropy coder to compress said difference, —encode said current read by the compressed difference, and —repeat the forgoing steps with said cur