Providing nucleotide sequence data

In a sequencer device which includes a processor and which receives a microarray comprising a plurality of capture oligonucleotide probes, each of the capture oligonucleotide probes being complementary in sequence to portions of a target nucleic acid and comprising two portions, said portions of the capture oligonucleotide probe being separated by a non-target complementary sequence label, and optionally an immobilization moiety, each of the portions of the capture oligonucleotide probe adapted to capture a specific sequence of a fragment of nucleic acids, the microarray comprising a chip encoding information or a label storing information for determining a relationship between a site on the microarray and reference sequences or an expected sequence associated with the capture oligonucleotide probes in the site, a method for providing nucleotide sequence data, the method comprising:

• hybridizing said capture oligonucleotide probe with a sample comprising a nucleic acid target molecule, wherein said target nucleic acid molecule comprises a sequence which is at least partially complementary to the capture oligonucleotide probe, the sequence of said capture oligonucleotide probe being at least partially complementary to the sequence of said fragment of nucleic acids, the sequence of said capture oligonucleotide probe being capable of capturing said fragment of nucleic acids by hybridization;
• circularizing said nucleic acid target molecule by use of a polymerase activity;
• amplifying said circularized nucleic acid target molecule;
• reading the information encoded by the chip or stored in the label of the microarray;
• with the processor, receiving basic nucleotide sequence data comprising a determined sequence of identifiers for nucleotides of a fragment of nucleic acids and probe data comprising position data of capture oligonucleotide probes in the microarray, the probe data including position data of the capture oligonucleotide probe that has captured the fragment of nucleic acids;
• with the processor, determining an expected sequence of the fragment of nucleic acids by converting the probe data into the expected sequence with the information read from the microarray to interrelate the probe data and the expected sequence, the probe data including information on the location of the determined sequence of the nucleic acid target molecule on a reference genome obtained by a method for determining the sequence of a target nucleic acid molecule linked to genomic position information of said target nucleic acid molecule, wherein said sequence of the capture oligonucleotide probe is not the same as the expected sequence, comprising:
• determining the sequence of the amplified nucleic acid target molecules by generating a sequence read of at least 2 nucleotides;
• identifying the sequence of the non-target complementary sequence label;
• identifying the nucleotide sequence of the capture oligonucleotide probe adjacent to the non-target complementary sequence label;
• identifying the location of the sequence of the capture oligonucleotide probe on the reference genome, the expected sequence being defined by interrelating the information on said location on the reference genome with the corresponding sequence of the reference genome;
• and
• outputting the nucleotide sequence data and a reference to the expected sequence, including providing a combination of (i) the determined sequence of identifiers of the nucleic acid target molecule and (ii) information on its location on the reference genome.

A sequencer device comprising:

• a microarray comprising a plurality of capture oligonucleotide probes, each of the capture oligonucleotide probes being complementary in sequence to portions of a target nucleic acid molecule and comprising two portions, said portions of the capture oligonucleotide probe being separated by a non-target complementary sequence label, and optionally an immobilization moiety, each of the portions of the capture oligonucleotide probe being adapted to capture a specific sequence of a fragment of nucleic acids, the capture oligonucleotide probes hybridizing with fragments of nucleic acids in the nucleic acid sample, the basic nucleotide sequence data generated by circularizing said nucleic acid target molecule by use of a polymerase activity and amplifying said circularized nucleic acid target molecule, the microarray comprising a chip encoding information or a label storing information for identifying a relationship between a site on the microarray and reference sequences or an expected sequence associated with the capture oligonucleotide probes in the site;
• a sequencing unit which reads the information encoded by the chip or stored in the label of the microarray and generates basic nucleotide sequence data, the sequencing unit receiving the microarray, the basic nucleotide sequence data comprising a determined sequence of identifiers for nucleotides of a fragment of nucleic acids and probe data, the probe data including position data of a respective capture oligonucleotide probe that has captured the fragment of nucleic acids;
• a pre-processing unit which receives basic nucleotide sequence data from the sequencing unit and interrelates the probe data with an expected sequence using the information read from the microarray to generate enriched nucleotide sequence data, the enriched nucleotide sequence data comprising a determined sequence of identifiers and the expected sequence or a reference to the expected sequence;
• an alignment unit which receives the enriched nucleotide sequence data and aligns the determined sequence of identifiers to a reference nucleotide sequence, including performing a string match comparison to see if the determined sequence matches the expected sequence and thereafter performing a regular alignment algorithm only if no exact match is found in the string match comparison;
• wherein the sequence device generates nucleotide sequence data comprising the determined sequence of identifiers and a reference to the expected sequence.