1. A method of characterizing biological material in a sample containing genetic material from a plurality of organisms, the method comprising: performing probabilistic methods that compare a plurality of metagenomic fragment reads obtained from the sample with a plurality of genome reads from a reference database containing genomic identities of organisms and produce probabilistic results; and determining the identities of organisms contained in the sample at least to the species level using the probabilistic results; wherein the method steps are performed using a processor and memory.