The eDNA-Container App: A Simple-to-Use Cross-Platform Package for the Reproducible Analysis of eDNA Sequencing Data

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 o...

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Bibliographic Details
Published in:Applied sciences 2024-03, Vol.14 (6), p.2641
Main Authors: Wheeler, David, Brancalion, Lillian, Kawasaki, Akitomo, Rourke, Meaghan L.
Format: Article
Language:English
Subjects:
Biological diversity
Biological monitoring
biosecurity
Cloning
Docker
Ecologists
environmental DNA
GUI
Internet
Linux
Metadata
Public software
QIIME2
Quality control
Software
Taxonomy
Technology application
User interface
Windows operating system
Work stations
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Summary: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.
ISSN:2076-3417
2076-3417
DOI:10.3390/app14062641