Conclusions
Our results show that brute force sequencing can serve as a simple and
efficient approach for prey metabarcoding of consumers that are less
known to science or difficult to dissect. Exactly how many extra reads
one should ask for to offset the losses to consumer sequencing depends
on multiple often unknown factors like copy number variation, life cycle
and seasonal parameters. We therefore suggest sequencing deeper than
what is strictly required based on an arbitrary ratio (e.g. with
expectancy of 99% consumer reads), as this approach is more
cost-efficient than resequencing samples with low coverage.