Systems and methods for analyzing sequence data

A method, comprising:

• using at least one computer hardware processor to perform:
• obtaining a plurality of sequence reads previously obtained from one or more genetic samples;
• obtaining, from at least one non-transitory computer-readable storage medium, a directed acyclic graph (DAG) data structure, wherein the DAG data structure comprises a plurality of nodes connected by a plurality of edges, the plurality of nodes including a first node included in a first path of a plurality of paths in the DAG data structure, the first node representing a first nucleotide sequence stored as a first string of one or more symbols;
• aligning at least some of the plurality of sequence reads to the DAG data structure;
• identifying, based on results of the aligning, one or more paths of the plurality of paths, the identifying comprising:
• determining support values for nodes in the first path based on the results of the aligning, the support values for the first node being indicative of a number of sequence reads aligned to the first string;
• determining a first support value for the first path based on the support values for the nodes in the first path;
• and
• including the first path in the one or more paths when the first support value exceeds a first threshold;
• and
• outputting at least one of the one or more identified paths.

A system, comprising:

• at least one computer hardware processor;
• and
• at least one non-transitory computer-readable storage medium storing processor executable instructions that, when executed by the at least one computer hardware processor, cause the at least one computer hardware processor to perform:
• obtaining a plurality of sequence reads previously obtained from one or more genetic samples;
• obtaining, from at least one non-transitory computer-readable storage medium, a directed acyclic graph (DAG) data structure, wherein the DAG data structure comprises a plurality of nodes connected by a plurality of edges, the plurality of nodes including a first node included in a first path of a plurality of paths in the DAG data structure, the first node representing a first nucleotide sequence stored as a first string of one or more symbols;
• aligning at least some of the plurality of sequence reads to the DAG data structure;
• identifying, based on results of the aligning, one or more paths of the plurality of paths, the identifying comprising:
• determining support values for nodes in the first path based on the results of the aligning, the support values for the first node being indicative of a number of sequence reads aligned to the first string;
• determining a first support value for the first path based on the support values for the nodes in the first path;
• and
• including the first path in the one or more paths when the first support value exceeds the first threshold;
• and
• outputting at least one of the one or more identified paths.

At least one non-transitory computer-readable storage medium storing processor executable instructions that, when executed by at least one computer hardware processor, cause the at least one computer hardware processor to perform:

• obtaining a plurality of sequence reads previously obtained from one or more genetic samples;
• obtaining, from at least one non-transitory computer-readable storage medium, a directed acyclic graph (DAG) data structure, wherein the DAG data structure comprises a plurality of nodes connected by a plurality of edges, the plurality of nodes including a first node included in a first path of a plurality of paths in the DAG data structure, the first node representing a first nucleotide sequence stored as a first string of one or more symbols;
• aligning at least some of the plurality of sequence reads to the DAG data structure;
• identifying, based on results of the aligning, one or more paths of the plurality of paths, the identifying comprising:
• determining support values for nodes in the first path based on the results of the aligning, the support values for the first node being indicative of a number of sequence reads aligned to the first string;
• determining a first support value for the first path based on the support values for the nodes in the first path;
• and
• including the first path in the one or more paths when the first support value exceeds the first threshold;
• and
• outputting at least one of the one or more identified paths.