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Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
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SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data
Yoann Dufresne1,2, Franck Lejzerowicz1,3, Laure Apotheloz Perret-Gentil1
1Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205, Geneva, Switzerland.
BMC Bioinformatics
|February 21, 2019
Summary
SLIM is a new web application simplifying environmental DNA metabarcoding analysis with an intuitive GUI. It automates complex data processing, making biodiversity surveys more accessible and reproducible for researchers.
Area of Science:
- Ecology
- Bioinformatics
- Genomics
Background:
- Environmental DNA (eDNA) metabarcoding is crucial for biodiversity assessment.
- High-throughput sequencing generates vast datasets requiring efficient analysis pipelines.
- Current tools often demand bioinformatic expertise, limiting accessibility and reproducibility.
Purpose of the Study:
- To develop a user-friendly, automated pipeline for eDNA metabarcoding data analysis.
- To enhance the accessibility of complex bioinformatics workflows for biodiversity research.
- To improve the reproducibility of eDNA metabarcoding studies.
Main Methods:
- Introduction of SLIM, an open-source web application with a Graphic User Interface (GUI).
- Integration of established bioinformatics software for seamless data processing.
- Module-centered design for flexibility and extensibility.
- Pipeline configuration saving for reproducible analysis.
Main Results:
- SLIM simplifies the creation and execution of eDNA metabarcoding analysis pipelines.
- The GUI facilitates processing from raw sequencing data to an annotated OTU-to-sample matrix.
- The application supports diverse metabarcoding scenarios and allows for custom extensions.
Conclusions:
- SLIM is designed for both non-specialists and advanced users, offering a user-friendly yet flexible solution.
- The tool enhances the reproducibility of eDNA metabarcoding analyses.
- Open-source code and documentation are available on GitHub, with a demonstration server provided.
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