K-mer based strain typing

A method for generating a k-mer based strain type mapping, the method comprising:

• receiving a set of nucleotide sequence data, the nucleotide sequence data including a plurality of nucleotide sequence data structures each corresponding to a separate microbial strain to be analyzed;
• generating a k-mer profile for each nucleotide sequence data structure, the k-mer profile including a set of k-mers derived from the corresponding nucleotide sequence data structure and count values corresponding to each k-mer of the set of k-mers, the count values indicating the number of times the corresponding k-mer occurs in the set of k-mers;
• and
• comparing a first k-mer profile to at least one other k-mer profile to determine a similarity score between the first k-mer profile and the at least one other k-mer profile, the similarity score indicating a relationship mapping of the respective microbial strains corresponding to the first k-mer profile and the at least one other k-mer profile.

A computer system configured for generating a k-mer based strain type mapping, the computer system comprising:

• one or more processors;
• and
• one or more hardware storage devices having stored thereon computer-executable instructions which are executable by the one or more processors to cause the computer system to perform at least the following:
• receive a set of nucleotide sequence data, the nucleotide sequence data including a plurality of nucleotide sequence data structures each corresponding to a separate microbial strain to be analyzed;
• for each nucleotide sequence data structure, generate a k-mer profile configured with a length of about 18-60 bases, the k-mer profile including a set of k-mers derived from the corresponding nucleotide sequence data structure and count values corresponding to each k-mer of the set of k-mers, the count values indicating the number of times the corresponding k-mer occurs in the set of k-mers;
• filter the k-mer profiles in order to reduce the number of k-mers within each compared k-mer profile;
• and
• compare a first k-mer profile to at least one other k-mer profile to determine a similarity score between the first k-mer profile and the at least one other k-mer profile, the similarity score indicating a relationship mapping of the respective microbial strains corresponding to the first k-mer profile and the at least one other k-mer profile.