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.