bio-workflows-edna-pipeline
End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal, denoising with OBITools3 or DADA2, contamination filtering, taxonomy assignment, Hill number diversity, and constrained ordination. Use when processing environmental DNA samples for biodiversity assessment or ecological surveys.
npx skills add BioTender-max/awesome-bio-agent-skills --skill edna-pipeline --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: DADA2 1.30+, FastQC 0.12+, MultiQC 1.21+, cutadapt 4.4+, phyloseq 1.46+, vegan 2.6+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # eDNA Metabarcoding Pipeline **"Process my eDNA samples from raw reads to community ecology"** → Orchestrate primer removal, denoising (OBITools3 or DADA2), contamination filtering, taxonomy assignment, Hill number diversity estimation, and constrained ordination for species-environment analysis. Complete workflow from raw amplicon sequences to community ecology analysis, supporting both OBITools3 and DADA2 processing paths. ## Pipeline Overview ``` Raw amplicon FASTQ (demultiplexed) | v [1. QC] ------------------> FastQC / MultiQC quality assessment | v [2. Primer Removal] ------> Cutadapt (remove forward + reverse primers) | | | +---> QC: reads per sample >1000 | +--- P
- Version Compatibility
- Pipeline Overview
- Step 1: Quality Assessment
- Step 2: Primer Removal
- QC Checkpoint: Demultiplexing
- Step 3: Paired-End Merging and Denoising
- Path A: OBITools3
- Path B: DADA2 (R)
- QC Checkpoint: Denoising
- Step 4: Contamination Filtering
- R (decontam)
- Tag-jumping removal
- QC Checkpoint: Decontamination
- Step 5: Taxonomy Assignment
fastqc -t 8 -o fastqc_output/ raw_reads/*.fastq.gz multiqc fastqc_output/ -o multiqc_report/ Adapter sequences are marker-specific; examples below for common eDNA markers COI (Leray primers mlCOIintF / jgHCO2198) cutadapt -g GGWACWGGWTGAACWGTWTAYCCYCC -G TAIACYTCIGGRTGICCRAARAAYCA \ for f in trimmed/*_R1.fastq.gz; do echo "$sample: $count reads" done Import paired FASTQ into OBITools3 DMS obi import --fastq-input trimmed/reads_R1.fastq.gz reads/reads1
What does the bio-workflows-edna-pipeline skill do?
End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal, denoising with OBITools3 or DADA2, contamination filtering, taxonomy assignment, Hill number diversity, and constrained ordination. Use when processing environmental DNA samples for biodiversity assessment or ecological surveys.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill edna-pipeline --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.