bio-microbiome-taxonomy-assignment
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-taxonomy-assignment --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+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+ 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. # Taxonomy Assignment **"Assign taxonomy to my ASVs"** → Classify amplicon sequence variants against reference databases (SILVA, GTDB, UNITE) using naive Bayes or exact-matching approaches for taxonomic annotation. - R: `dada2::assignTaxonomy()` with SILVA/GTDB reference - CLI: `qiime feature-classifier classify-sklearn` for QIIME2 workflows ## DADA2 Naive Bayes Classifier ```r library(dada2) seqtab_nochim <- readRDS('seqtab_nochim.rds') # SILVA for 16S (download from https://zenodo.org/record/4587955) taxa <- assignTaxonomy(seqtab_nochim, 'silva_nr99_v138.1_train_set.fa.gz', multithread = TRUE) # Add species-level (exact matching) taxa <- addSpecies(taxa, 'silva_species_assignme
- Version Compatibility
- DADA2 Naive Bayes Classifier
- GTDB for 16S
- UNITE for ITS (Fungi)
- QIIME2 Feature Classifier
- VSEARCH Exact Matching
- RDP Classifier
- IDTAXA (DECIPHER) - Often More Accurate
- Confidence Filtering
- Combine into phyloseq
- Database Comparison
- Related Skills
Train classifier (one-time) qiime feature-classifier fit-classifier-naive-bayes \ Classify ASVs qiime feature-classifier classify-sklearn \ Faster but requires exact or near-exact matches vsearch --usearch_global asv_seqs.fasta \
What does the bio-microbiome-taxonomy-assignment skill do?
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-taxonomy-assignment --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.