Metagenomics for microorganism identification

A computer-implemented method for microorganism identification, the method comprising:

• receiving long-read nucleic acid fragment sequence data (LRS data) obtained from the sample;
• performing taxonomic classification of the LRS data to assign one or more taxonomic identifiers to each record on the LRS data;
• determining an abundance levels of a plurality of reference genomes based on the taxonomic identifiers of the LRS data;
• aligning the LRS data with the subset of the reference genomes, wherein the subset of the reference genomes demonstrated abundance in the sample reaching or exceeding a predefined abundance level;
• performing coverage analysis based on the alignment of the LRS data with the candidate genomes;
• identifying one or more microorganism species present in the sample based on the coverage estimate.

A method for detecting infection by one or more microorganism in a subject, the method comprising:

• determining long-read nucleic acid fragment sequence data (LRS data) from a sample obtained from the subject;
• performing taxonomic classification of the LRS data to assign one or more taxonomic identifiers to each record on the LRS data;
• determining abundance levels of a plurality of reference genomes based on the taxonomic identifiers of the LRS data;
• aligning the LRS data with the candidate genomes in response to one or more candidate genomes of the plurality of reference genomes reaching or exceeding a predefined abundance level;
• performing coverage analysis based on the alignment of the LRS data with the candidate genomes;
• determining an identity of one or more microorganism present in the sample based on the coverage analysis so as to detect infection by the one or more microorganism in the subject.