Data from: From benchtop to desktop: important considerations when designing amplicon sequencing workflows

Amplicon sequencing has been the method of choice in many high-throughput
DNA sequencing (HTS) applications. To date there has been a heavy focus on
the means by which to analyse the burgeoning amount of data afforded by
HTS. In contrast, there has been a distinct lack of attention paid to
considerations surrounding the importance of sample preparation and the
fidelity of library generation. No amount of high-end bioinformatics can
compensate for poorly prepared samples and it is therefore imperative that
careful attention is given to sample preparation and library generation
within workflows, especially those involving multiple PCR steps. This
paper redresses this imbalance by focusing on aspects pertaining to the
benchtop within typical amplicon workflows: sample screening, the target
region, and library generation. Empirical data is provided to illustrate
the scope of the problem. Lastly, the impact of various data analysis
parameters is also investigated in the context of how the data was
initially generated. It is hoped this paper may serve to highlight the
importance of pre-analysis workflows in achieving meaningful, future-proof
data that can be analysed appropriately. As amplicon sequencing gains
traction in a variety of diagnostic applications from forensics to
environmental DNA (eDNA) it is paramount workflows and analytics are both
fit for purpose.