Systems and methods for grouping and collapsing sequencing reads

A computer-implemented method for determining a nucleotide sequence from nucleotide sequencing reads, comprising:

• receiving a plurality of first nucleotide sequencing reads;
• for each first nucleotide sequencing read:
• generating a plurality of first identifier subsequences from a first identifier sequence of the first nucleotide sequencing read;
• for each first identifier subsequence, determining a plurality of hashes using a plurality of hash functions;
• generating a first signature for the first nucleotide sequencing read comprising a plurality of first signature hashes each for a different first position, wherein each first signature hash is selected from the hashes determined for the plurality of first identifier subsequences at the first position of the first signature hash;
• and
• assigning the first nucleotide sequencing read to a first particular bin of a first data structure based on the first signature;
• and
• determining a nucleotide sequence for each first particular bin of the first data structure with one or more first nucleotide sequencing reads assigned.

A system for identifying similar nucleotide sequencing reads, comprising:

• non-transitory memory configured to store:
• executable instructions, a first hash data structure and a second hash data structure for storing a plurality of pairs of sequencing reads;
• and
• a hardware processor programmed by the executable instructions to perform:
• receiving a pair of a first query nucleotide sequencing read and a second query nucleotide sequencing read, wherein the first query nucleotide sequencing read and the second query nucleotide sequencing read are paired-end nucleotide sequencing reads;
• generating (i) a plurality of first query identifier subsequences from the first query nucleotide sequencing read, and (ii) a plurality of second query identifier subsequences from the second query nucleotide sequencing read;
• determining (i) for each first query identifier subsequence, a plurality of first query hashes, and (ii) for each second query identifier subsequence, a plurality of second query hashes, using a plurality of hash functions;
• generating a first query signature for the first query nucleotide sequencing read comprising a plurality of first query signature hashes each for a different first position, and (ii) a second query signature for the second query nucleotide sequencing read comprising a plurality of second query signature hashes each for a different second position, wherein each first query signature hash is selected from the first hashes determined for the plurality of first query identifier subsequences at the first position of the first query signature hash, and wherein each second query signature hash is selected from the second hashes determined for the plurality of second query identifier subsequences at the second position of the second query signature hash;
• retrieving (i) one or more first stored pairs from the first hash data structure using the first query signature, and (ii) one or more second stored pairs from the second hash data structure using the second query signature, wherein each first stored pair comprises a first stored nucleotide sequencing read and a second stored nucleotide sequencing read that are paired-end nucleotide sequencing reads, and wherein each second stored pair comprises a first stored nucleotide sequencing read and a second stored nucleotide sequencing read that are paired-end nucleotide sequencing reads;
• and
• determining, for each pair of a first stored nucleotide sequencing read and a second stored nucleotide sequencing read present in both the first stored pairs and second stored pairs, the first stored nucleotide sequencing read and the second stored nucleotide sequencing read of the pair as being similar to the first query sequencing read and the second query sequencing read, respectively.

A method for identifying similar nucleotide sequencing reads, comprising:

• receiving a first query nucleotide sequencing read;
• generating a plurality of first query identifier subsequences from the first query nucleotide sequencing read;
• for each first query identifier subsequence, determining a plurality of first query hashes using a plurality of hash functions;
• generating a first query signature for the first nucleotide sequencing read comprising a plurality of first query signature hashes each for a different first position, wherein each first query signature hash is selected from the first hashes determined for the plurality of first query identifier subsequences at the first position of the first query signature hash;
• and
• retrieving one or more first stored nucleotide sequencing reads from a first hash data structure using the first query signature, wherein each of the first stored nucleotide sequencing reads is similar to the first query nucleotide sequencing read.