Systems and methods for SNP analysis and genome sequencing

A non-transitory computer-readable storage medium for identifying one or more species in an undifferentiated environmental sample comprising a plurality of nucleic acid sequences corresponding to one or more species, the non-transitory computer-readable storage medium storing instructions configured to be executed by a system comprising a processor to cause the system to:

• generate and store at least one generated index of the one or more indices;
• receive reference data representing a reference nucleic acid sequence associated with the generated index;
• identify, in the reference data, a first reference subsequence of the reference nucleic acid sequence associated with the generated index, wherein the first reference subsequence is retrieved from a first position of the nucleic acid sequence associated with the generated index;
• compute a hash of the first reference subsequence to determine a first corresponding element of the generated index;
• and
• store, in the first corresponding element of the generated index, position data reflecting the first position and indicating the reference nucleic acid sequence associated with the generated index;
• load one or more indices, including the at least one generated index, representing a plurality of reference nucleic acid sequences, wherein the one or more indices each comprises a respective plurality of elements, each element corresponding to a potential nucleic acid sequence permutation, wherein the one or more indices are limited, based on statistical methods regarding which permutations are most likely to occur, to less than a total possible number of permutations,
• receive data comprising a plurality of data structures, each of the plurality of data structures digitally representing a respective nucleic acid sequence;
• for each of the nucleic acid sequences in the received data, attempt to align the nucleic acid sequence to each of reference nucleic acid sequences using the one or more indices;
• for each of the nucleic acid sequences in the received data, determine, using the one or more indices, whether the nucleic acid sequence is successfully aligned to any one or more of the reference nucleic acid sequences;
• for each one of the reference nucleic acid sequences, calculate a respective alignment ratio based on the number of nucleic acid sequences that were determined to be successfully aligned to the respective reference nucleic acid sequence and based on the total number of nucleic acid sequences in the received data;
• and
• generate and store the plurality of calculated alignment ratios for the received data.

A method for identifying one or more species in an undifferentiated environmental sample comprising a plurality of nucleic acid sequences corresponding to one or more species, the method performed at a system comprising a processor and memory, the method comprising:

• generating and storing at least one generated index of the one or more indices;
• receiving reference data representing a reference nucleic acid sequence associated with the generated index;
• identifying, in the reference data, a first reference subsequence of the reference nucleic acid sequence associated with the generated index, wherein the first reference subsequence is retrieved from a first position of the nucleic acid sequence associated with the generated index;
• computing a hash of the first reference subsequence to determine a first corresponding element of the generated index;
• and
• storing, in the first corresponding element of the generated index, position data reflecting the first position and indicating the reference nucleic acid sequence associated with the generated index;
• loading one or more indices, including the at least one generated index, representing a plurality of reference nucleic acid sequences, wherein the one or more indices each comprises a respective plurality of elements, each element corresponding to a potential nucleic acid sequence permutation, wherein the one or more indices are limited, based on statistical methods regarding which permutations are most likely to occur, to less than a total possible number of permutations,
• receiving data comprising a plurality of data structures, each of the plurality of data structures digitally representing a respective nucleic acid sequence;
• for each of the nucleic acid sequences in the received data, attempting to align the nucleic acid sequence to each of reference nucleic acid sequences using the one or more indices;
• for each of the nucleic acid sequences in the received data, determining, using the one or more indices, whether the nucleic acid sequence is successfully aligned to any one or more of the reference nucleic acid sequences;
• for each one of the reference nucleic acid sequences, calculating a respective alignment ratio based on the number of nucleic acid sequences that were determined to be successfully aligned to the respective reference nucleic acid sequence and based on the total number of nucleic acid sequences in the received data;
• and
• generating and storing the plurality of calculated alignment ratios for the received data.