Classification performance of combined 100 nt single-read predictions, as compared to the best performing paired-end configurations.

<p>We combined predictions made for different 100 nt fragments of the same sequence, by selecting the prediction with the highest confidence score at the genus level (or the lowest common level available). We evaluated the performance, at ranks genus and family (left and right panels, respectively), of combinations of fragments from the V3 and V4 regions (top and bottom panels, respectively) with fragments from each of the other regions examined, and compared it to the performance of the V3 and V4 100 nt paired-end configurations (pointed to by arrows). We used the results of leave-k-out tests classifying the LTP sequences to determine confidence score thresholds for a set of desired false prediction rate (FPR) values (x axis), so that the FPR would be at most the desired value. We then used these thresholds to calculate the classification coverage of sequences from environmental (uncultured) bacteria that corresponds to the desired FPR (y axis). <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053608#pone.0053608.s006" target="_blank">Figure S6</a> compares the performance of the combinations for the ranks order, class, and phylum.