Sequence analysis method, sequence analysis apparatus, reference sequence generation method, reference sequence generation apparatus, program, and storage medium

A sequence analysis apparatus comprising:

• at least one processing device configured to:
• obtain a first plurality of read sequences which are read from a first nucleic acid sequence, wherein the first plurality of read sequences comprise 40 to 200 giga-bases (Gb);
• at a first time, determine the first nucleic acid sequence by aligning the first plurality of read sequences with reference to a single reference sequence, wherein the single reference sequence comprises at least a first rearrangement sequence and a second rearrangement sequence that is different from the first rearrangement sequence, wherein an entirety of the second rearrangement sequence is appended after an entirety of the first rearrangement sequence within the single reference sequence to form a continuous string including at least the first rearrangement sequence and the second rearrangement sequence;
• at a second time after the first time, determine that a new known mutation information exists in a mutation information database, wherein a creation date for the new known mutation information corresponds to a time that is after the first time;
• update the reference sequence to add a third rearrangement sequence related to the new known mutation information by appending an entirety of the third rearrangement sequence after at least one of the entirety of the first rearrangement sequence or the entirety of the second rearrangement sequence within the single reference sequence to create an updated single reference sequence that is formed as a continuous string including at least the first rearrangement sequence, the second rearrangement sequence, and the third rearrangement sequence;
• obtain a second plurality of read sequences which are read from a second nucleic acid sequence;
• and
• determine the second nucleic acid sequence by aligning the second plurality of read sequences with reference to the updated single reference sequence.

A reference sequence generation apparatus configured to generate a reference sequence to be used for determining a nucleic acid sequence of a plurality of read sequences which is read by a sequencer and which comprises 40 to 200 giga-bases (Gb), the reference sequence generation apparatus comprising:

• at least one processing device configured to:
• obtain a first rearrangement sequence and a second rearrangement sequence;
• at a first time, generate a reference sequence in which the first rearrangement sequence and the second rearrangement sequence are connected in one piece, wherein an entirety of the second rearrangement sequence is appended after an entirety of the first rearrangement sequence within the single reference sequence to form a continuous string including at least the first rearrangement sequence and the second rearrangement sequence;
• at a second time after the first time, determine that a new known mutation information exists in a mutation information database, wherein a creation date for the new known mutation information corresponds to a time that is after the first time;
• and
• update the reference sequence to add a third rearrangement sequence related to the new known mutation information by appending an entirety of the third rearrangement sequence after at least one of the entirety of the first rearrangement sequence or the entirety of the second rearrangement sequence within the single reference sequence to create an updated single reference sequence that is formed as a continuous string including at least the first rearrangement sequence, the second rearrangement sequence, and the third rearrangement sequence.