Initial processing of Illumina data for dietary DNA metabarcoding

By Bethan Littleford-Colquhoun

A huge debt of gratitude to Beth for organizing a google drive folder that shares our strategy for initial processing of dietary DNA metabarcoding data. This directory provides template documents and code that we use to download paired-end read data from our dietary metabarcoding workflows, assemble forward and reverse reads, perform initial quality controls, and evaluate sequencing success. There is also a tutorial for how to upload sample data to SRA for archiving, which we have started to do routinely. Some details are specific to our dietary analysis sequencing workflow and/or the specific sequencing service that we use, plus we have particular sample naming schemes that we use, but it should be pretty straightforward to adapt for a variety of similar goals.