Biodiv Sci ›› 2019, Vol. 27 ›› Issue (5): 567-575.DOI: 10.17520/biods.2018211

• Methodology • Previous Articles     Next Articles

EPPS, a metabarcoding bioinformatics pipeline using Nextflow

Li Yiyuan()*,C. Molik David,E. Pfrender Michael   

  1. Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46554, USA)Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46554, USA
  • Received:2018-08-01 Accepted:2019-03-05 Online:2019-05-20 Published:2019-05-20

Abstract:

Metabarcoding helps to quickly assess biodiversity. In this study, we discuss popular metabarcoding analytical tools and parameter settings. We also develop a metabarcoding bioinformatics pipeline, EPPS, to process data from quality control of raw reads to biodiversity comparisons between samples using a pipeline building program, Nextflow. The EPPS pipeline can summarize the time and memory cost of each process in the pipeline. We also apply the pipeline on a test dataset and a public dataset from a previous study. The result suggests that this pipeline can reliably analyze metabarcoding data and facilitate pipeline sharing of metabarcoding studies.

Key words: environmental DNA, USEARCH, Trimmomatic, principal component analysis