Recommended experimental designs.

a<p>Primer would be used only for amplification, not for sequencing.</p>b<p>The lowest confidence value threshold (CT) that is consistent with an FPR of 5% (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053608#s3" target="_blank">methods</a>).</p>c<p>Coverage (in percentage units) observed for the confidence threshold in environmental sequences.</p>d<p>Median number of predictions in the interval [CT.CT+4] was smaller than 10.</p>e<p>Results for 100 nt and 120 nt paired end configurations were practically identical for this region, as we encountered few V3 amplicons that were longer than 100 nt (all in the environmental sequences).</p>f<p>CT for these cases is lower than that of a higher level/s, and a sequence can thus be classified at the current level but not at the higher taxonomic levels. We find that the classification of such sequences is associated with a high error rate and our recommendation is to exclude them, and have adjusted coverage accordingly.