bio-workflows-edna-pipeline
OfficialEnd-to-end eDNA metabarcoding workflow.
Authorstellaromics
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Automates the end-to-end eDNA metabarcoding analysis from raw amplicon reads to ecological interpretation, reducing manual tool chaining and ensuring reproducible QC, denoising, and downstream analyses.
Core Features & Use Cases
- End-to-end pipeline supporting OBITools3 and DADA2 workflows, including QC, primer removal, denoising, chimera removal, and contamination filtering.
- Taxonomy assignment with marker-appropriate reference databases, diversity analysis with iNEXT, and constrained ordination with vegan.
- Supports multiple markers (COI, 12S, ITS, rbcL, 18S) for ecological surveys and biodiversity monitoring.
- Includes parameter recommendations, troubleshooting guidance, and a ready-to-run usage guide.
Quick Start
Process my environmental DNA samples from raw reads to community ecology outputs using the full eDNA metabarcoding workflow.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: bio-workflows-edna-pipeline Download link: https://github.com/stellaromics/fast-bioinfo/archive/main.zip#bio-workflows-edna-pipeline Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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