Methods, Systems and Computer Readable Storage Media for Generating Accurate Nucleotide Sequences

A method of processing sequence data to generate a consensus sequence, comprising:

• receiving one or more groups of aligned sequence data, the aligned sequence data including one or more aligned reads of sequence data, each read including sequence data disposed at a plurality of main positions and a plurality of secondary position regions including a plurality of secondary positions disposed adjacent to each main position;
• correcting the sequence data disposed at one or more main positions in each read based on the sequence data disposed in each adjacent secondary position region;
• determining a group of one or more reads with each main position without diversity based on a diversity confidence score for each group of the corrected aligned sequence data, the diversity confidence score being based on a frequency of each nucleotide disposed at each main position in the group;
• determining legitimate sequence data based on each secondary position region of the group of one or more reads with each main position without diversity in which one or more nucleotides are disposed;
• and
• generating a consensus sequence incorporating sequence data disposed at main positions without diversity and the legitimate sequence data disposed at each secondary position region for each group of one or more reads with each main position without diversity.

A system for processing sequence data to generate a consensus sequence, comprising:

• a memory;
• and
• a processor, wherein the processor is configured to cause:
• determining a group of one or more reads with each main position without diversity from a group of one or more aligned reads based on diversity status of each main position of the group of one or more aligned reads, each group including sequence data disposed at a plurality of main positions and a plurality of secondary position regions disposed adjacent to the main positions, the diversity status being based on a frequency of one or more nucleotides and/or diversity confidence score of one or more non-consensus nucleotides disposed at each main position in each group;
• determining legitimate sequence data from each second position region having one or more nucleotides for each group of one or more reads without diversity;
• and
• generating a consensus sequence including sequence data disposed at each main position without diversity and legitimate sequence data disposed at each secondary position region for each group of one or more reads with each main position without diversity.