Advantages of multiplexing several amplicons
Increasing the number of monitored amplicons to four increased our ability to robustly distinguish samples from two locations (Figure 3-4 and Supplementary Figure S6-S11 ). Multiplexing could be used in other ways, for example to monitor several organisms in the same environment, or to increase read coverage profiling of single genetic markers such as 16S . In addition, there is a technical benefit in sequencing multiple different targets together, because a lack of sequence diversity can cause Illumina base-calling issues .