eDNAFlow

eDNAFlow processes environmental DNA (eDNA) high-throughput sequencing data to generate Zero-Radius Operational Taxonomic Units (ZOTUs) and perform taxonomic assignment for biodiversity monitoring.

Key Features:

• Automation and Workflow Management: Integrates state-of-the-art applications to automate processing of single-end and paired-end raw sequences within a workflow.
• ZOTU Generation: Produces curated and non-curated Zero-Radius Operational Taxonomic Units (ZOTUs) from eDNA sequence data.
• Taxonomy Assignment: Includes an in-house Python script to assign taxonomy to ZOTUs with user-specified thresholds for Lowest Common Ancestor (LCA) determination.
• Scalability and Portability: Built on Nextflow and Singularity to support execution on local machines, cloud environments, and high-performance computing (HPC) clusters.
• Reproducibility: Uses Singularity containers to provide consistent software environments for reproducible analyses.

Scientific Applications:

• Biodiversity Monitoring: Processes eDNA data to detect and characterize species composition in environmental samples.
• Coral Diversity Biomonitoring: Applied to coral diversity biomonitoring to assess coral-associated taxa from environmental samples.
• Large-Scale Ecological Studies: Demonstrated on a dataset of 154 samples, supporting large-scale ecological and environmental research.

Methodology:

Nextflow orchestrates integrated bioinformatics tools and Singularity containers provide consistent environments; the pipeline processes single-end and paired-end raw sequences to generate curated and non-curated ZOTUs and assigns taxonomy using an in-house Python script with user-defined LCA thresholds.