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bio-microbiome-taxonomy-assignment

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawDiscoveryReadingbio-microbiome-taxonomy-assignment🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiometaxonomic

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-taxonomy-assignment

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

R: dada2::assignTaxonomy() with SILVA/GTDB reference.
CLI: qiime feature-classifier classify-sklearn for QIIME2 workflows.
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.
taxa <- assignTaxonomy(seqtab_nochim, 'silva_nr99_v138.1_train_set.fa.gz', multithread = TRUE).

Source Doc

Excerpt From SKILL.md

DADA2 Naive Bayes Classifier

library(dada2)

seqtab_nochim <- readRDS('seqtab_nochim.rds')

## Add species-level (exact matching)

taxa <- addSpecies(taxa, 'silva_species_assignment_v138.1.fa.gz')

## GTDB-formatted database (better for environmental samples)

taxa_gtdb <- assignTaxonomy(seqtab_nochim, 'GTDB_bac120_arc53_ssu_r220_fullTaxo.fa.gz',
                            multithread = TRUE)