Split-read alignment by intelligently identifying and scoring candidate split groups
AssigneeIllumina Software, Inc.
InventorMichael Ruehle
Life of this patent
Estimating the term…
Abstract
The present disclosure relates to systems, non-transitory computer-readable media, and methods for efficiently identifying and selecting split groups corresponding to one or more nucleotide reads. Generally, split groups comprise chains of fragments forming split-alignments of one read. The disclosed system utilizes dynamic programming to generate and evaluate candidate split groups. The disclosed system can generate split group scores for each of the candidate split groups. To generate the split group scores, the disclosed system considers fragment alignment scores and geometries of fragment alignments within the candidate split groups. The disclosed systems select a predicted split group from the candidate split groups based on the split group scores.
Claims20
A computer-implemented method comprising:
- identifying one or more nucleotide reads corresponding to a genomic region of a genomic sample;
- determining candidate split groups comprising fragment alignments corresponding to the one or more nucleotide reads;
- generating split group scores for split alignments of the candidate split groups with a reference genome;
- and
- selecting, for nucleobase calling of the genomic region, a predicted split group from the candidate split groups based on the split group scores.
A system comprising:
- at least one processor;
- and
- a non-transitory computer-readable medium comprising instructions that, when executed by the at least one processor, cause the system to:
- identify one or more nucleotide reads corresponding to a genomic region of a genomic sample;
- determine candidate split groups comprising fragment alignments corresponding to the one or more nucleotide reads;
- generate split group scores for split alignments of the candidate split groups with a reference genome;
- and
- select, for nucleobase calling of the genomic region, a predicted split group from the candidate split groups based on the split group scores.
A non-transitory computer-readable medium comprising instructions that, when executed by at least one processor, cause a computing device to:
- identify one or more nucleotide reads corresponding to a genomic region of a genomic sample;
- determine candidate split groups comprising fragment alignments corresponding to the one or more nucleotide reads;
- generate split group scores for split alignments of the candidate split groups with a reference genome;
- and
- select, for nucleobase calling of the genomic region, a predicted split group from the candidate split groups based on the split group scores.
Dependencies are inferred from the claim text.