## 1 Introduction  
Environmental DNA (eDNA) is genetic material originating from organisms in the environment, including shed cells, secretions, and whole microorganisms [1]. The high-throughput sequencing of eDNA has proven to be a powerful tool in ecology and biosecurity as it can be used to monitor the presence of species, assess the impact of human activities on ecosystems, and track the spread of invasive species [2, 3, 4, 5]. eDNA sampling is also less invasive than traditional biodiversity monitoring methods such as electrofishing, and being relatively inexpensive, it is a cost-effective option for large-scale sampling surveys. Due to the ease of sampling, eDNA can be used to survey a wide range of habitats, including those that are difficult to access, such as deep lakes and remote streams [6, 7, 8].  
There are several bioinformatics tools that are commonly used for eDNA analysis including _search_, _usearch_, _MiFish_, and _QIIME2_[9, 10, 11, 12, 13]. These tools clean and process short-read sequencing data, assign species to reference sequences, and quantify the species diversity of each sample. However, the unfamiliar command-line interface adopted by many of these packages can make it difficult for wet lab staff and field ecologists to use the software effectively. Additionally, Microsoft Windows versions of these packages are often not available due to the popularity of UNIX/Linux amongst developers of scientific software.  
_QIIME2_ is one of the most popular software packages for DNA barcoding-based community analyses [14, 15, 16]. This open-source package includes plugins for workflows such as _cutadapt_ for quality trimming, _DADA2_ for denoising and building amplified sequence variants (ASVs), as well as tools for building custom taxonomic classifiers [17; 18; 19]. This package was developed to run natively on Linux systems; however, a command-line interface can be accessed on Microsoft Windows via Windows Subsystem for Linux (WSL) or using a Linux virtual machine. WSL and virtual machines are relatively advanced computer utilities, which could hinder the wider adoption of this package for eDNA analysis.  
_Docker_ is a software platform that allows developers to build, run, and share applications in containers. The containers are lightweight, standalone packages of software that include everything needed to run an application, including code, system libraries, and program settings. _Docker_ makes it easy to deploy applications because it provides a consistent way to package and run software regardless of the underlying operating system. These features have made _Docker_ an important tool for scientific software development because applications will generate consistent outputs irrespective of the underlying computer frameworks being utilized [20; 21; 22; 23].  
Here, we introduce the _eDNA-container app_, which is an eDNA analysis pipeline that uses _QIIME2_ for amplicon sequence variant generation and taxonomic assignment. The application includes a graphics user interface (GUI) that allows the user to configure runtime and quality control parameters, select primers, and utilize custom taxonomic databases. Key pipeline outputs, such as sequence quality plots and ASV generation statistics are automatically included in a final PDF report. The final feature counts and taxonomic assignments across all samples are provided in a comma-separated file (CSV) that can be viewed using spreadsheet software (i.e., _Excel_ or _LibreOffice Calc_). This free open-source application is available on the Docker hub, and developers can access the underlying _python_ and _bash_ code by directly cloning the projects GitHub repository.