Systems and methods for analyzing nucleic acid sequences

A computer implemented method for nucleic acid sequence assembly, the method comprising:

• obtaining a nucleic acid sequence read;
• obtaining a reference sequence;
• iteratively selecting anchor sequences comprising differing lengths of a contiguous portion of the nucleic acid sequence read, wherein each anchor sequence begins at a same location on the nucleic acid sequence read;
• mapping, using a processor, the anchor sequence to the reference sequence using an approximate string mapping method that allows for a set number of mismatches with the reference sequence and produces at least one match with the reference sequence, wherein the iteratively selecting and mapping of the anchor sequence is performed until a number of matches of the anchor sequence to the reference sequence is less than a threshold number;
• mapping, using the processor, a remaining portion of the nucleic acid sequence read to the reference sequence using an ungapped local alignment method that produces an alignment of the remaining portion extending from the at least one match to map the nucleic acid sequence read to the reference sequence;
• generating an indexed binary file that stores the mapping of the anchor sequence and remaining portion to the reference sequence;
• filtering the indexed binary file to generate a filtered indexed binary file, the filtered indexed binary file comprising nucleic acid sequence reads that are mapped to target enriched regions in the reference sequence;
• and
• performing a resequencing analysis on the filtered indexed binary file to assemble a nucleotide sequence based on the nucleotide sequence read.

A non-transitory computer-readable storage medium comprising:

• a program with instructions to be executed by a processor so as to perform a method for nucleic acid sequence assembly, the method comprising:
• receiving a nucleic acid sequence read;
• obtaining a reference sequence;
• iteratively selecting anchor sequences comprising differing lengths of a contiguous portion of the nucleic acid sequence read, wherein each anchor sequence begins at a same location on the nucleic acid sequence read;
• mapping the anchor sequence to the reference sequence using an approximate string mapping method that allows for a set number of mismatches with the reference sequence and produces at least one match with the reference sequence, wherein the iteratively selecting and mapping of the anchor sequence is performed until a number of matches of the anchor sequence to the reference sequence is less than a threshold number;
• mapping a remaining portion of the read to the reference sequence using an ungapped local alignment method that produces an alignment of the remaining portion extending from the at least one match to map the nucleic acid sequence read to the reference genome;
• generating an indexed binary file that stores the mapping of the anchor sequence and remaining portion to the reference sequence;
• filtering the indexed binary file to generate a filtered indexed binary file, the filtered indexed binary file comprising nucleic acid sequence reads that are mapped to target enriched regions in the reference sequence;
• and
• performing a resequencing analysis on the filtered indexed binary file to assemble a nucleotide sequence based on the nucleotide sequence read.

A computer implemented method for nucleic acid sequence assembly, the method comprising:

• obtaining a nucleic acid sequence read;
• obtaining a reference sequence;
• iteratively selecting anchor sequences comprising differing lengths of a contiguous portion of the nucleic acid sequence read, wherein each anchor sequence begins at a same location on the nucleic acid sequence read;
• mapping, using a processor, the anchor sequence to the reference sequence using an approximate string mapping method that allows for a set number of mismatches with the reference sequence and produces at least one match with the reference sequence, wherein the iteratively selecting and mapping of the anchor sequence is performed until a number of matches of the iteratively selected contiguous portion to the reference sequence is less than a threshold number;
• mapping, using the processor, a remaining portion of the nucleic acid sequence read to the reference sequence using an ungapped local alignment method that produces an alignment of the remaining portion extending from the at least one match to map the nucleic acid sequence read to the reference sequence;
• generating a binary file that stores the mapping of the anchor sequence and remaining portion to the reference sequence;
• extracting, from the binary file, one or more alignments for the nucleic acid sequence reads from the mapping of the anchor sequence and remaining portion to the reference sequence;
• calculating alignment scores for the one or more alignments extracted from the binary file, wherein the alignment score represents a quality of the alignment;
• classifying a portion of the one or more alignments as duplicates based on the alignment scores;
• and
• marking, in the binary file, the portion of the one or more alignments as duplicates to assemble a nucleotide sequence based on the nucleotide sequence read.