Preparing manuscript files for dietary DNA data

Working with dietary DNA metabarcoding data? Unsure how to concisely summarize your workflow for publication? Tired of all the effort required to format your data tables for archiving in Dryad, supplementary materials, or other archives? The lab has posted new code to our GitHub repository that will help you solve all of these problems.

The new repository for "Step 5" of our standard dietary DNA metabarcoding pipeline provides code to prepare 'phyloseq' objects for use in the R package of the same name. You can find an overview of our standard workflow and links to all component parts on the Software & Data page of the Kartzinel Lab's website.

This workflow takes all of the extensive and complex files generated by using our lab's dietary DNA metabarcoding pipeline and formats them for downstream ecological analyses. The code follows relatively standard processing steps that we have found useful in our extensive work involving dietary data from herbivores (e.g., using the trnL-P6 marker). However, most steps are optional or customizable using different parameters based on the unique needs and goals of a variety of projects.

The workflow includes code to filter your full sample set to include only specific subsets of data, if desired. It also facilitates the removal of samples with low read counts, which are occasional even in the most successful sequencing projects. 

Our workflow continues on to rarefy samples to equal sequencing depth, and merge data with external taxonomic or ecological data as needed.

Throughout this process, the code generates comprehensive data summaries that you can report in your manuscripts to clearly describe and justify the workflow that you follow. It also exports both pre- and post-rarefaction OTU tables as permanent records suitable for manuscript supplementary materials, ultimately producing a clean, analysis-ready phyloseq object alongside documentation of key metrics for reporting in scientific publications and permanent repositories.