Pros and cons of metabarcoding approaches
The ability to tag and index amplicons to fully harvest the power of high-throughput sequencing comes at a price; the labelling and pooling of hundreds of PCR replicates is highly complex and entails costs associated with preventing, detecting, and eliminating errors and biases. None of the metabarcoding approaches presented here is perfect; rather each of them has pros and cons. Below, we outline the advantages and disadvantages, specifically addressing issues related to cross-contamination risk, PCR amplification efficiency, chimera formation, tag-jumping, index-misassignment, cost, and workload. The issues associated with each metabarcoding strategy are important to keep in mind for choosing a metabarcoding strategy and for designing laboratory workflows and interpreting results.