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bio-microbiome-functional-prediction

Maintainer FreedomIntelligence · Last updated April 1, 2026

Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.

OpenClawNanoClawAnalysisReproductionbio-microbiome-functional-prediction🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiomepredict

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • CLI: picrust2_pipeline.py -s seqs.fna -i table.biom -o output/.
  • Predict functional pathways from my 16S data" → Infer metagenome functional content from marker gene (16S/ITS) ASV tables using phylogenetic placement and gene content prediction. CLI: picrust2_pipeline.py -s seqs.fna -i table.biom -o output/.
  • otu <- as.data.frame(otu_table(ps)) if (!taxa_are_rows(ps)) otu <- t(otu) write.table(otu, 'asv_table.tsv', sep = '\t', quote = FALSE).

Source Doc

Excerpt From SKILL.md

Prepare Input Files

library(phyloseq)
library(Biostrings)

ps <- readRDS('phyloseq_object.rds')

## Export ASV sequences as FASTA

seqs <- refseq(ps)  # Or extract from ASV names if stored there
writeXStringSet(seqs, 'asv_seqs.fasta')

Full pipeline (place sequences, predict functions, metagenome inference)

picrust2_pipeline.py
-s asv_seqs.fasta
-i asv_table.tsv
-o picrust2_output
-p 4
--stratified
--per_sequence_contrib

Use cases

  • Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • amplicon-processing - Generate ASV input
  • metagenomics/functional-profiling - Direct shotgun-based profiling
  • pathway-analysis/kegg-pathways - KEGG pathway enrichment

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