Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-microbiome-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Microbiome: 16S/ITS amplicon or shotgun → diversity → differential.

OpenClawNanoClawAnalysisReproductionbio-workflows-microbiome-pipeline🧠 bioos extended suitebioos extended bioinformatics suitemicrobiome

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

path <- 'raw_reads' silva_train <- 'silva_nr99_v138.1_train_set.fa.gz' silva_species <- 'silva_species_assignment_v138.1.fa.gz' metadata_file <- 'sample_metadata.csv.
fnFs <- sort(list.files(path, pattern = '_R1_001.fastq.gz', full.names = TRUE)) fnRs <- sort(list.files(path, pattern = '_R2_001.fastq.gz', full.names = TRUE)) sample_names <- sapply(strsplit(basename(fnFs), '_'), [, 1).

Source Doc

Excerpt From SKILL.md

Complete R Workflow

library(dada2)
library(phyloseq)
library(ALDEx2)
library(vegan)
library(ggplot2)

## Setup filtered files

filtFs <- file.path('filtered', paste0(sample_names, '_F_filt.fastq.gz'))
filtRs <- file.path('filtered', paste0(sample_names, '_R_filt.fastq.gz'))

## === 2. FILTER & TRIM ===

out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs,
                     truncLen = c(240, 160), maxN = 0, maxEE = c(2, 2),
                     truncQ = 2, rm.phix = TRUE, compress = TRUE, multithread = TRUE)

Use cases

Use bio-workflows-microbiome-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-microbiome-pipeline to sequencing, variant, or omics analysis tasks.