End-to-end workflow to generate cleaned consensus sequences from multiplexed amplicons sequenced with Nanopore sequencing technology. Includes read basecalling, quality control, data filtering, read demultiplexing, consensus sequence generation, and a data summary. The workflow assumes that individual samples have been uniquely indexed to allow highly multiplexed sequencing runs. The demultiplexing code is annotated to indicate different demultiplexing strategies utilized in the study. This workflow was used in the publication "Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa", and the last section of the workflow consists of a custom R script that generates summary statistics specific to the publication. Overall, this workflow can be modified to suit multiple markers, and is applicable to teaching in a classroom setting with the accompanying docker image.