How grace-hoang/automated-microbiome-r-pipeline works
This repository is an automated R pipeline for bacterial 16S amplicon analysis. Its principal workflow takes paired FASTQ reads through quality assessment, primer removal, filtering, ASV inference and taxonomy assignment, then builds phyloseq data for downstream analyses. The README documents read tracking, phylogenetic-tree construction, rarefaction, diversity, composition and differential-abundance results, plus resumable intermediate RDS files. The graph follows those documented stages; source excerpts were unavailable, so exact calls and some downstream data dependencies cannot be verified.
Main entry points: main.R Pipeline runner · 10_phyloseq_build.R Phyloseq construction · 07_chimera_length_filter.R Chimera filtering · 12_rarefaction.R Rarefaction
Components 24
Configuration
- Pipeline parameters
R/00_parameters.R - Helper functions
R/01_helper_functions.R - Pipeline runner
main.R
Sequence processing
- Quality profiles
R/02_quality_profiles.R - Primer removal
R/03_primer_removal.R - Filter and trim
R/04_filter_trim.R - Learn errors
R/05_learn_errors.R - Denoise and merge
R/06_denoise_merge.R - Chimera filtering
R/07_chimera_length_filter.R - Read tracking
R/08_read_tracking.R
Community modeling
- Taxonomic assignment
R/09_taxonomy.R - Phyloseq construction
R/10_phyloseq_build.R - Phylogenetic tree
R/11_phylogenetic_tree.R - Rarefaction
R/12_rarefaction.R
Downstream analysis
- Alpha diversity
R/13_alpha_diversity.R - Beta diversity
R/14_beta_diversity.R - Relative abundance
R/15_relative_abundance.R - Differential abundance
R/16_ancombc.R
Other components
- Analyst
- FASTQ reads
- Sample metadata
- SILVA training set
- cutadapt
- Saved results
Connections 48
- Analyst → Pipeline parameters: configures
- Analyst → Pipeline runner: runs
- Pipeline runner → Quality profiles: runs
- Pipeline runner → Primer removal: runs
- Pipeline runner → Filter and trim: runs
- Pipeline runner → Learn errors: runs
- Pipeline runner → Denoise and merge: runs
- Pipeline runner → Chimera filtering: runs
- Pipeline runner → Read tracking: runs
- Pipeline runner → Taxonomic assignment: runs
- Pipeline runner → Phyloseq construction: runs
- Pipeline runner → Phylogenetic tree: runs
- Pipeline runner → Rarefaction: runs
- Pipeline runner → Alpha diversity: runs
- Pipeline runner → Beta diversity: runs
- Pipeline runner → Relative abundance: runs
- Pipeline runner → Differential abundance: runs
- FASTQ reads → Quality profiles: provides reads
- Quality profiles → Primer removal: guides trimming
- FASTQ reads → Primer removal: provides reads
- Primer removal → Filter and trim: trimmed reads
- cutadapt → Primer removal: removes primers
- Filter and trim → Learn errors: filtered reads
- Learn errors → Denoise and merge: error models
- Denoise and merge → Chimera filtering: ASV table
- Chimera filtering → Read tracking: read counts
- Chimera filtering → Taxonomic assignment: filtered ASVs
- SILVA training set → Taxonomic assignment: training set
- Chimera filtering → Phyloseq construction: filtered ASVs
- Taxonomic assignment → Phyloseq construction: taxonomy
- Sample metadata → Phyloseq construction: sample data
- Phyloseq construction → Phylogenetic tree: builds tree
- Phyloseq construction → Rarefaction: rarefies
- Rarefaction → Alpha diversity: diversity input
- Rarefaction → Beta diversity: diversity input
- Rarefaction → Relative abundance: composition input
- Rarefaction → Differential abundance: analysis input
- Pipeline runner → Saved results: saves checkpoints
- Quality profiles → Saved results: saves outputs
- Primer removal → Saved results: saves outputs
- Filter and trim → Saved results: saves outputs
- Learn errors → Saved results: saves outputs
- Denoise and merge → Saved results: saves outputs
- Chimera filtering → Saved results: saves outputs
- Read tracking → Saved results: saves outputs
- Taxonomic assignment → Saved results: saves outputs
- Phyloseq construction → Saved results: saves outputs
- Phylogenetic tree → Saved results: saves outputs