Adapter trimming and determination in next generation sequencing data analysis

A computer-implemented system for adapter trimming in sequencing data analysis, comprising:

• one or more hardware processors;
• one or more data storage devices storing instructions that, when executed by the one or more hardware processors, cause the one or more hardware processors to perform operations, the operations comprising:
• selecting, based on a plurality of match scores, one or more of:
• a first alignment from (a) aligning a tail of a first sequencing read to a head of a second sequencing read at one or more first positions;
• a second alignment from (b) aligning the tail of the second sequencing read to the head of the first sequencing read at one or more second positions;
• a third alignment from (c) aligning a first adapter to the tail of the first sequencing read at one or more third positions;
• and
• a fourth alignment from (d) aligning a second adapter to the tail of the second sequencing read at one or more fourth positions,
• wherein each of the plurality of match scores is based on a first number of matched bases and a second number of total bases;
• generating a first consensus position using the first alignment and the third alignment and a second consensus position using the second alignment and the fourth alignment;
• and
• determining a trimming position based on the first consensus position, the second consensus position, a first consensus match score, and a second consensus match score.

A computer-implemented method for adapter determination in sequencing data analysis, comprising:

• obtaining, by a processor, a plurality of pair-end sequencing reads, each pair-end sequencing read comprising a first and second sequencing read, wherein each of the first and second sequencing read comprise a sequence of nucleotide bases;
• determining, by the processor, an adapter position based on:
• a first alignment from (a) aligning a tail of a first sequencing read to a head of a second sequencing read at one or more first positions;
• and
• a second alignment from (b) aligning the tail of the second sequencing read to the head of the first sequencing read at one or more second positions;
• obtaining, by the processor, a plurality of adapter sequences from the plurality of pair-end sequencing reads based on the determined adapter position;
• repetitively performing one or more operations until a stopping criterion is met, comprising:
• selecting a seed adapter sequence from the plurality of adapter sequences;
• determining one or more adapter sequences among the plurality of adapter sequences that satisfy a similarity threshold in comparison with the seed adapter sequence;
• and
• determining, for each base position, a base of A, G, C, or T/U based on a corresponding count of different bases at the corresponding base position of the one or more determined adapter sequence and a predetermined threshold, thereby generating an individual candidate adapter;
• and
• removing the seed adapter sequence and the one or more determined adapter sequences from the plurality of adapter sequences.

A computer-implemented system for adapter determination in sequencing data analysis, comprising:

• one or more hardware processors;
• one or more data storage devices storing instructions that, when executed by the one or more hardware processors, cause the one or more hardware processors to perform operations, the operations comprising:
• obtaining, by a processor, a plurality of pair-end sequencing reads, each pair-end sequencing read comprising a first and second sequencing read, wherein each of the first and second sequencing read comprise a sequence of nucleotide bases;
• selecting, by the processor and based on a plurality of match scores, one or more of:
• a first alignment from (a) aligning a tail of the first sequencing read to a head of the second sequencing read at one or more first positions;
• a second alignment from (b) aligning the tail of the second sequencing read to the head of the first sequencing read at one or more second positions, wherein each of the plurality of match scores is based on a first number of matched bases and a second number of total bases;
• determining, by the processor, an adapter position based on the selected one or more of the first alignment and the second alignment.