1. The eDNA-Container App: A Simple-to-Use Cross-Platform Package for the Reproducible Analysis of eDNA Sequencing Data
- Author
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David Wheeler, Lillian Brancalion, Akitomo Kawasaki, and Meaghan L. Rourke
- Subjects
environmental DNA ,QIIME2 ,Docker ,GUI ,biosecurity ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
The analysis of environmental DNA (eDNA) is a powerful and non-invasive method for monitoring the presence of species in ecosystems. However, ecologists and laboratory staff can find it challenging to use eDNA analysis software effectively due to the unfamiliar command-line interfaces used by many of these packages. Therefore, we developed the eDNA-container app, a free and open-source software package that provides a simple user-friendly interface for eDNA analysis. The application is based on the popular QIIME2 library and is distributed as a Docker image. The use of Docker makes it compatible with a wide range of operating systems and facilitates the reproducible analysis of data across different laboratories. The application includes a point-and-click user interface for selecting sequencing files, configuring parameters, and accessing the results. Key pipeline outputs, such as sequence quality plots, denoising, and ASV generation statistics, are automatically included in a PDF report. This open-source and freely available analysis package should be a valuable tool for scientists using eDNA in biodiversity and biosecurity applications.
- Published
- 2024
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