Pathogen identification and antibiotic characterization in metagenomic samples

摘要

Identification of pathogens in metagenomic samples and characterization of antibiotics Extracting (12), sequencing the extracted DNA and thereby generating a set of reads (14), assigning the set of reads to a known pathogen to assign the reads to the pathogen. Comparing to a database of genomics (22);-generating a pool of reads, including reads assigned to the pathogen (26), and assembling the pooled reads to generate a "contig" (26). 28),-To check whether the generated contig contains the marker, Compare that to include (30). The method may further comprise comparing the reading to a second database to assign the reading to a marker, wherein the reading is assigned to the marker if the reading completely falls within the marker or if the reading spans the marker. And, the pool also includes a read assigned to the marker, whereby the contig comprises assembling (24) the read assigned to the pathogen and the read assigned to the marker. [Selection diagram] FIG.