Patent ID: 8478544

Claim:
A method of characterizing biological material in a sample containing genetic material from a plurality of organisms, the method comprising: (a) generating a plurality of unassembled metagenomic fragment reads by sequencing metagenomic fragments extracted from the sample; (b) creating a reference word table for a plurality of genome reads from a reference database containing genomic identities of organisms comprising: (b1) splitting each of the genome reads into reference words, (b2) creating a list of reference words from the reference words for each of the genome reads, and (b3) storing the lists of reference words in a reference word table; (c) creating a list of sample sequence words for each of the plurality of unassembled metagenomic fragment reads comprising: (c1) splitting each of the unassembled metagenomic fragment reads into sample sequence words, and (c2) creating a list of sample sequence words from the sample sequence words for each of the unassembled metagenomic fragments; (d) 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 (e) determining the identities of organisms contained in the sample at least to the species level using the probabilistic results; wherein the reference word table creating step, the lists of sample sequence words creating step, the probabilistic method performing step, and determining step are performed using one or more processors and one or more memories.