Systems and methods for analyzing viral nucleic acids

A method for analyzing a virus having a viral genome comprising a plurality of viral sequences, the method comprising using at least one processor to perform:

• accessing a viral DNA reference directed acyclic graph (DAG) from at least one non-transitory memory, the viral DNA reference DAG representing at least some of the plurality of viral sequences of the viral genome and comprising nodes and edges connecting the nodes, the nodes including a first node and a second, wherein:
• the first node is stored as a first object in the at least one non-transitory memory, the first object comprising a first symbol string representing a first viral sequence of the viral sequences,
• the second node is stored as a second object in the at least one non-transitory memory, the second object comprising a second symbol string representing a second viral sequence of the viral sequences, and
• the first object further comprises a first list of one or more pointers to one or more adjacent objects, the first list of one or more pointers including a pointer to the second object;
• obtaining a plurality of sequence reads from a sample containing viral nucleic acid;
• aligning one or more sequence reads of the plurality of sequence reads to the viral DNA reference DAG, at least in part by determining alignment scores between the one or more sequence reads and symbol strings associated with nodes of the viral DNA reference DAG, wherein determining an alignment score for the second node comprises, for a first symbol in the second symbol string associated with the second node, determining the alignment score for the second node based on an alignment score associated with the first node;
• determining, based on the aligned one or more sequence reads, an identity of a virus in the sample;
• and
• providing a report that includes the identity of the virus in the sample.

A system for analyzing a virus having a viral genome comprising a plurality of viral sequences, the 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 a method comprising:
• obtaining a plurality of sequence reads from a sample containing viral nucleic acid;
• accessing a viral DNA reference directed acyclic graph (DAG) representing at least some of the plurality of viral sequences of the viral genome, the viral DNA reference DAG comprising nodes and edges connecting the nodes, the nodes including a first node and a second, wherein:
• the first node is stored as a first object in the at least one non-transitory computer-readable storage medium, the first object comprising a first symbol string representing a first viral sequence of the viral sequences,
• the second node is stored as a second object in the at least one non-transitory computer-readable storage medium, the second object comprising a second symbol string representing a second viral sequence of the viral sequences, and
• the first object further comprises a first list of one or more pointers to one or more adjacent objects, the first list of one or more pointers including a pointer to the second object;
• aligning one or more sequence reads of the plurality of sequence reads from the sample to the viral DNA reference DAG, at least in part by determining alignment scores between the one or more sequence reads and symbol strings associated with nodes of the viral DNA reference DAG, wherein determining an alignment score for the second node comprises, for a first symbol in the second symbol string associated with the second node, determining the alignment score for the second node based on an alignment score associated with the first node;
• determining, based on the aligned one or more sequence reads, an identity of a virus in the sample;
• and
• providing a report that includes the identity of the virus in the sample.

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 a method comprising:

• obtaining a plurality of sequence reads from a sample containing viral nucleic acid;
• accessing a viral DNA reference directed acyclic graph (DAG) representing at least some of the plurality of viral sequences of a viral genome, the viral DNA reference DAG comprising nodes and edges connecting the nodes, the nodes including a first node and a second, wherein:
• the first node is stored as a first object in the at least one non-transitory computer-readable storage medium, the first object comprising a first symbol string representing a first viral sequence of the viral sequences,
• the second node is stored as a second object in the at least one non-transitory computer-readable storage medium, the second object comprising a second symbol string representing a second viral sequence of the viral sequences, and
• the first object further comprises a first list of one or more pointers to one or more adjacent objects, the first list of one or more pointers including a pointer to the second object;
• aligning one or more sequence reads of the plurality of sequence reads from the sample to the viral DNA reference DAG, at least in part by determining alignment scores between the one or more sequence reads and symbol strings associated with nodes of the viral DNA reference DAG, wherein determining an alignment score for the second node comprises, for a first symbol in the second symbol string associated with the second node, determining the alignment score for the second node based on an alignment score associated with the first node;
• determining, based on the aligned one or more sequence reads, an identity of a virus in the sample;
• and
• providing a report that includes the identity of the virus in the sample.