eDNA pipeline showcase (epps) using Nextflow from the PfrenderLab @ University of Notre Dame. It takes a directory with fastq files and a primer file and automatically does quality filtering, primer removal, merging, and OTU clustering.

./nextflow epps_v190209.nf -with-timeline

Yiyuan Li, David C. Molik, Michael E. Pfrender (2019) EPPS, a metabarcoding bioinformatics pipeline using Nextflow. Biodiversity Science, 27(5), 567-575.

http://www.biodiversity-science.net/EN/10.17520/biods.2018211