Systems and methods for genomic analysis
AssigneeArc Bio, LLC
InventorsAlejandro QUIROZ ZARATE, Roberto OLIVARES-AMAYA, Thomas James WATSON, Jr., Helen Cecile VAN AGGELEN, Eduardo CORONADO SROKA, Carlos Antonio ANGULO SERMENO, Fernando FIMBRES JURADO, Abraham SOLIS GARCIA-INDA, Fernando FONTOVE HERRERA, Pablo G. COSTE
Life of this patent
Estimating the term…
Abstract
Provided herein are methods for aligning raw genetic sequence data generated by a sequencing device. Also provided herein are methods and systems for quantifying the probability that possible alignments for one or more read pairs are correct, for calling known variants, and for detecting novel structural variants.
Claims35
1-9. (canceled)
A method to identify novel variants, the method comprising:
- (a) obtaining a plurality of sequence reads;
- (b) aligning the plurality of sequence reads against a graph reference, wherein the graph reference comprises known variants represented by alternate paths;
- and
- (c) using a subset of the plurality of sequence reads which abnormally align against one or more alternate paths to identify novel variants.
(canceled)
(canceled)
(canceled)
26-29. (canceled)
33-35. (canceled)
37-39. (canceled)
42-144. (canceled)
A method for calling variants, the method comprising:
- (a) retrieving a read;
- (b) generating a k-mer profile from the read;
- and
- (c) querying the k-mer profile to an index of k-mer profiles from a reference sequence with alternate paths to call variants.
147-216. (canceled)
Dependencies are inferred from the claim text.