title: human oropharyngeal metagenome
design: OP swabs were swiped in a 1.5 ml tube containing 500 l sterile PBS. 200 l of the bacterial suspension was used for DNA extraction using Qiacube running the DNA Mini extraction program. Human reads were removed in two runs of BBmap v38.84: a first course run to remove a majority of human reads (parameters: mode fast = true, minratio=0.9; maxindel=3, minhits=2, kmer length=14). The second run used default parameters for more sensitivity in removing remaining human reads.