Similar protocols

Protocol publication

[…] her purified with AMPure beads (Beckman Coulter, Brea, CA), and molar equivalents were determined for each sample with a Bioanalyzer 2100 HS DNA kit (Agilent Technologies, Santa Clara, CA). Samples were pooled into equimolar proportions and sequenced on 314 chips with an Ion Torrent PGM according to the manufacturer’s instructions (Life Technologies, Grand Island, NY) (). Resulting sequence reads were removed from the analysis if they were <130 nt, had any bar code or primer errors, contained any ambiguous characters, or contained any stretch of >6 homopolymers. Sequences were assigned to their respective samples on the basis of their 10-nt bar code sequences and analyzed further with Qiime (). Briefly, representative OTUs from each set were chosen at a minimum sequence identity of 97% with UClust () and aligned with PyNast () against the GreenGenes database (). Multiple alignments then were used to create phylogenies with FastTree (), and taxonomy was assigned to each OTU with the RDP classifier (, ). PCOA was performed on the basis of beta diversity by using weighted UniFrac distances (). Qiime was also used to calculate Shannon diversity indices., To assess whether viromes had significant overlap within or between subjects or subject groups, we performed a permutation test based on resampling (10,000 iterations). We simulated the distribution of the fraction of shared virome homologues from different subjects, biogeographic sites, or oral health statuses that were randomly chosen across all of the sub […]

Pipeline specifications

Software tools QIIME, UCLUST, PyNAST