Patent ID: 11929149
Assignee: ARC BIO, LLC
Field: Computer technology (Electrical engineering)
Classification: CPC G  C | IPC C  G

Claim 18:
19. A method for calling variants, the method comprising:
(a) retrieving, using a hardware processor, a sequencing read generated from a sample by a sequencing device;
(b) generating, using the hardware processor, a k-mer profile from the read using a mask containing l's and one or more 0's to generate each k-mer from the sequencing read such that bases in the read corresponding to the one or more 0's are excluded from the k-mer;
(c) querying, using the hardware processor, the k-mer profile to an index of k-mer profiles, generated from a reference sequence with alternate paths using the mask, to call variants,
wherein each k-mer in the index of k-mer profiles that corresponds to at least one alternate path is stored with a unique pointer for each of the at least one alternate paths that points to a data structure associated with that alternate path, the data structure including a sequence associated with the alternate path, and a start offset and an end offset indicative of a location of the alternate path with respect to the reference sequence; and

(d) determining, using the hardware processor, a species or a strain present in the sample based on the called variants.