FRAMEWORK FOR IDENTIFYING SEQUENCE PATTERNS THAT CAUSE SEQUENCE-SPECIFIC ERRORS (SSEs)

A system comprising:

• one or more processors;
• and
• one or more storage devices storing instructions that, when executed by the one or more processors, cause the system to:
• identify a nucleotide sequence corresponding to one or more biological samples;
• computationally overlay a repeat pattern on the nucleotide sequence and produce an overlaid sample comprising a variant nucleotide at a target position and the repeat pattern at an offset position relative to the target position;
• generate, based on processing the overlaid sample through a variant filter operatively coupled to a sequencer instrument, one or more classification scores indicating likelihoods that the variant nucleotide at the target position in the overlaid sample is a true variant or a false variant;
• and
• classify, based on the one or more classification scores, the repeat pattern at the offset position in the overlaid sample as causing a sequence-specific error in the nucleotide sequence corresponding to the one or more biological samples.

A non-transitory computer readable storage medium storing instructions that, when executed by one or more processors, cause a system to:

• identify a nucleotide sequence corresponding to one or more biological samples;
• computationally overlay a repeat pattern on the nucleotide sequence and produce an overlaid sample comprising a variant nucleotide at a target position and the repeat pattern at an offset position relative to the target position;
• generate, based on processing the overlaid sample through a variant filter operatively coupled to a sequencer instrument, one or more classification scores indicating likelihoods that the variant nucleotide at the target position in the overlaid sample is a true variant or a false variant;
• and
• classify, based on the one or more classification scores, the repeat pattern at the offset position in the overlaid sample as causing a sequence-specific error in the nucleotide sequence corresponding to the one or more biological samples.

A computer-implemented method comprising:

• identifying a nucleotide sequence corresponding to one or more biological samples;
• computationally overlaying a repeat pattern on the nucleotide sequence and produce an overlaid sample comprising a variant nucleotide at a target position and the repeat pattern at an offset position relative to the target position;
• generating, based on processing the overlaid sample through a variant filter operatively coupled to a sequencer instrument, one or more classification scores indicating likelihoods that the variant nucleotide at the target position in the overlaid sample is a true variant or a false variant;
• and
• classifying, based on the one or more classification scores, the repeat pattern at the offset position in the overlaid sample as causing a sequence-specific error in the nucleotide sequence corresponding to the one or more biological samples.