SYSTEMS AND METHODS FOR IDENTIFYING MICROORGANISMS

摘要

The invention provides methods for identifying a microorganism by aligning sequence reads to a graph, such as a directed acyclic graph (DAG), that contains condensed sequence information of a conserved region from multiple known microorganisms. The DAG can be constructed by obtaining sequence information of known reference microorganisms. The DAG also includes the identities of the known microorganisms that correspond to particular paths. Sequence reads obtained from an unknown sample can thus be aligned to paths in the DAG using an alignment algorithm, and the identity of a microorganism in the sample can be determined based on which path in the DAG to which the sequence reads align best.

主权项

1. A method for identifying a microorganism, comprising:
obtaining a sequence of a conserved gene for each of a plurality of microorganisms; transforming, by a computer system comprising a processor coupled to a memory device, the sequences into a graph data structure comprising nodes connected by edges, wherein each microorganism is represented by a path through the graph data structure that contains the sequence of the conserved gene for that microorganism; obtaining sequence reads from a sample containing nucleic acid from at least one microorganism; determining optimal-scoring alignments between the sequence reads and one or more paths within the graph data structure; and identifying one or more identities of one or more microorganisms represented by the one or more paths.