bio-ecological-genomics-edna-metabarcoding - eDNA Metabarcoding Analysis
Process environmental DNA amplicon reads into species occurrence tables using OBITools3 and DADA2 with taxonomy assignment and contamination filtering.
Tags
Updated: 2026-06-30Capabilities
Typical Inputs
Typical Outputs
What this skill does
- trim primers
- align paired-end reads
- filter sequences
- dereplicate sequences
- denoise sequences
- remove chimeras
- assign taxonomy
- filter contaminants
- fit occupancy models
Inputs
- raw paired-end reads
- primer sequences
- reference database
- negative control samples
- DNA concentrations
Outputs
- species occurrence table
- taxonomy assignments
- occupancy estimates
Requirements
- R environment
- Python environment
- OBITools3
- DADA2
- cutadapt
- decontam
- JAGS