System and method for secondary analysis of nucleotide sequencing data

A system for sequencing polynucleotides, comprising:

• a sequencing apparatus configured to determine the nucleotide sequence of a polynucleotide;
• and
• a processor configured to control the sequencing apparatus and to execute instructions that perform a method comprising:
• receiving a first nucleotide subsequence of the polynucleotide;
• determining whether the first nucleotide subsequence aligns to a reference sequence at a first plurality of candidate locations beyond a threshold confidence level using a first process;
• receiving a second nucleotide subsequence of the polynucleotide from the sequencing apparatus, wherein the second nucleotide subsequence comprises the first nucleotide subsequence plus one or more additional nucleotides;
• comparing the one or more additional nucleotides in the second nucleotide subsequence to the reference sequence based in part on the first plurality of candidate locations, if the first nucleotide subsequence is aligned to the reference sequence beyond the threshold confidence level, or
• repeating the first process by aligning the entire second nucleotide subsequence to the reference sequence if the first nucleotide subsequence is not aligned to the reference sequence beyond the threshold confidence level.

A computer-implemented method for efficient sequencing of polynucleotides, comprising:

• receiving a first nucleotide subsequence of a read from a sequencing apparatus during a sequencing run of the first nucleotide subsequence;
• performing a secondary analysis of the first nucleotide subsequence of the read based on a reference sequence using a first process or a second process, wherein the first nucleotide subsequence comprises one or more additional nucleotides compared to a previous iteration, wherein the second process is more computationally efficient than the first process in performing the secondary analysis, wherein the first process aligns the entire first nucleotide subsequence to the reference sequence, wherein the second process aligns the one or more additional nucleotides to the reference sequence based in part on results from the previous iteration, and wherein the secondary analysis comprises:
• comparing the first nucleotide subsequence to the reference sequence to determine a first subsequence of the reference sequence that has a high degree of similarity to the first nucleotide subsequence;
• and
• determining if the sequencing apparatus should generate additional nucleotide reads.