Methods and Systems for Local Sequence Alignment

A non-transitory machine-readable storage medium comprising instructions which, when executed by a processor, cause the processor to perform a method for nucleic acid sequencing comprising:

• (a) exposing a plurality of template polynucleotide disposed in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith, to a series of flows of nucleotide species flowed according to a predetermined ordering;
• (b) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands;
• and
• (c) aligning the plurality of sequencing reads using an alignment process comprising a first set of alignment criteria or penalties that are based on biological changes in sequence and a second set of alignment criteria or penalties that are based on a sequencing error mode.

A system, including:

• a machine-readable memory;
• and
• a processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform a method for nucleic acid sequencing, comprising:
• (a) exposing a plurality of template polynucleotide disposed in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith, to a series of flows of nucleotide species flowed according to a predetermined ordering;
• (b) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands;
• and
• (c) aligning the plurality of sequencing reads using an alignment process comprising a first set of alignment criteria or penalties that are based on biological changes in sequence and a second set of alignment criteria or penalties that are based on a sequencing error mode.