EPPS, a metabarcoding bioinformatics pipeline using Nextflow
【Abstract】Metabarcoding helps to quickly assess biodiversity. In this study, we discussed the popular metabarcoding analytical tools and parameter settings. We also developed a metabarcoding bioinformatics pipeline, EPPS, to process the data from quality control of raw reads to biodiversity comparisons between samples using a pipeline building program, Nextflow. The EPPS pipeline could summarize the time and memory cost of each process in the pipeline. We also applied the pipeline on a test dataset and a public dataset from a previous study. The result suggested that this pipeline could reliably analyze metabarcoding data and facilitate pipeline sharing of metabarcoding studies.
【Keywords】 environmental DNA; USEARCH; Trimmomatic; principal component analysis;
(Translated by QI RS)
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