A method of detecting and identifying pathogens in a sample comprising a plurality of genetic sequences. A plurality of electronic sequence reads corresponding to the plurality of genetic sequences is received and sampled to form a sample set. The sample set is iteratively and electronically compared to a plurality of pathogen sequences to create a detection group, which populates a putative genome data structure. A distance score is measured between each electronic sequence read of the sampled set to each pathogen sequence of the putative genome data structure. A hit score is calculated by comparing the distance score to a threshold value. A plurality of clusters of the electronic sequence reads of the sample set is formed to maximize the cluster hit score and to minimize a difference in distance scores of the cluster. A respective taxonomic group assigned to electronic reads of the sample set after clustering is displayed.