Direct identification and measurement of relative populations of microorganisms with direct DNA sequencing and probabilistic methods

An apparatus for characterizing biological material in a sample containing genetic material from a plurality of organisms, the apparatus comprising:

• a processor and memory, wherein the processor and memory are configured to:
• (a) create a reference word table for a plurality of genome reads from a reference database containing genomic identities of organisms comprising:
• (a1) split each of the genome reads into reference words,
• (a2) create a list of reference words from the reference words for each of the genome reads, and
• (a3) store the lists of reference words in a reference word table;
• (b) create a list of sample sequence words for each of a plurality of unassembled metagenomic fragment reads generated by sequencing metagenomic fragments extracted from the sample comprising:
• (b1) split each of the unassembled metagenomic fragment reads into sample sequence words, and
• (b2) create a list of sample sequence words from the sample sequence words for each of the unassembled metagenomic fragments;
• (c) perform probabilistic methods that compare the sample sequence words in the lists of sample sequence words with the reference words in the lists of references words stored in the reference word table and produce probabilistic results;
• and
• (d) determine the identities of organisms contained in the sample at least to the species level using the probabilistic results.

A non-transitory computer-readable medium containing instructions that, when executed by a computer, cause the computer to execute the steps of:

• (a) creating a reference word table for a plurality of genome reads from a reference database containing genomic identities of organisms comprising:
• (a1) splitting each of the genome reads into reference words,
• (a2) creating a list of reference words from the reference words for each of the genome reads, and
• (a3) storing the lists of reference words in a reference word table;
• (b) creating a list of sample sequence words for each of a plurality of unassembled metagenomic fragment reads generated by sequencing metagenomic fragments extracted from a sample containing genetic material from a plurality of organisms comprising:
• (b1) splitting each of the unassembled metagenomic fragment reads into sample sequence words, and
• (b2) creating a list of sample sequence words from the sample sequence words for each of the unassembled metagenomic fragments;
• (c) performing probabilistic methods that compare the sample sequence words in the lists of sample sequence words with the reference words in the lists of references words stored in the reference word table and produce probabilistic results;
• and
• (d) determining the identities of organisms contained in the sample at least to the species level using the probabilistic results.