# tom-jenkins/maerl_whole_genome_resequencing architecture

> Architecture diagram of the GitHub repository tom-jenkins/maerl_whole_genome_resequencing, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-29). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/tom-jenkins/maerl_whole_genome_resequencing
- Repository: https://github.com/tom-jenkins/maerl_whole_genome_resequencing

## Overview

This is a research-analysis repository supporting a population-genomics study of two habitat-building coralline algae species and their responses to climate change. The visible scripts cover SNP quality control, ploidy and population structure, Fst, climate-data processing and RDA offset analyses, microbiota analysis, and figure generation. The tree and README do not document execution order or script-level data transfers, so the graph groups these analysis stages without asserting unsupported calls or pipelines.

Main entry points: [`GEA_01_Climate_Data.R`](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/GEA_01_Climate_Data.R) (Climate data processing), [`Microbiota_Analysis.R`](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/Microbiota_Analysis.R) (Microbiota analysis), [`SNP_01_QC_Filter.R`](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_01_QC_Filter.R) (SNP quality control), [`SNP_02_Allele_Balance_Ploidy.R`](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_02_Allele_Balance_Ploidy.R) (Allele balance and ploidy)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_genomics["Population genomics"]
  node_qc["SNP quality control<br/>[SNP_01_QC_Filter.R]"]
  node_ploidy["Allele balance and ploidy"]
  node_pc_structure["P. calcareum structure"]
  node_lc_structure["L. corallioides structure"]
  node_fst["Fst analysis<br/>[SNP_05_Fst.R]"]
  node_snp_outputs["SNP analysis outputs"]
end

subgraph group_climate["Climate adaptation"]
  node_climate_data["Climate and site data"]
  node_climate_process["Climate data processing"]
  node_pc_rda["P. calcareum RDA offset"]
  node_lc_rda["L. corallioides RDA offset"]
end

subgraph group_other["Supporting analyses"]
  node_microbiota_data["Kraken microbiota data"]
  node_microbiota["Microbiota analysis"]
  node_barcodes["DNA barcodes"]
  node_tree["Species tree"]
  node_figures["Figure generation<br/>[Figure_01.R]"]
end

node_researcher(("Researcher"))

node_researcher -->|"runs analysis"| node_qc
node_researcher -->|"runs analysis"| node_ploidy
node_researcher -->|"runs analysis"| node_pc_structure
node_researcher -->|"runs analysis"| node_lc_structure
node_researcher -->|"runs analysis"| node_fst
node_researcher -->|"runs analysis"| node_climate_process
node_researcher -->|"runs analysis"| node_pc_rda
node_researcher -->|"runs analysis"| node_lc_rda
node_researcher -->|"runs analysis"| node_microbiota
node_researcher -->|"runs analysis"| node_figures
node_climate_process -->|"processes data"| node_climate_data
node_microbiota -->|"analyzes data"| node_microbiota_data

click node_qc "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_01_QC_Filter.R"
click node_ploidy "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_02_Allele_Balance_Ploidy.R"
click node_pc_structure "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_03_Pcalcareum_Population_Structure.R"
click node_lc_structure "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_04_Lcorallioides_Population_Structure.R"
click node_fst "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_05_Fst.R"
click node_snp_outputs "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/outputs"
click node_climate_data "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/data/environmental_data"
click node_climate_process "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/GEA_01_Climate_Data.R"
click node_pc_rda "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/GEA_02_Pcalcareum_RDA_Offset.R"
click node_lc_rda "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/GEA_03_Lcorallioides_RDA_Offset.R"
click node_microbiota_data "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/data/kraken_results"
click node_microbiota "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/Microbiota_Analysis.R"
click node_barcodes "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/data/DNA_barcoding"
click node_tree "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/data/astral_results/busco_genes_ASTRAL_spp.tree"
click node_figures "https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/Figure_01.R"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_qc,node_ploidy,node_pc_structure,node_lc_structure,node_fst,node_snp_outputs toneBlue
class node_climate_data,node_climate_process,node_pc_rda,node_lc_rda toneAmber
class node_microbiota_data,node_microbiota,node_barcodes,node_tree,node_figures toneMint
class node_researcher toneIndigo
```

## Components

### Population genomics

- [SNP quality control](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_01_QC_Filter.R): `SNP_01_QC_Filter.R`
- [Allele balance and ploidy](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_02_Allele_Balance_Ploidy.R): `SNP_02_Allele_Balance_Ploidy.R`
- [P. calcareum structure](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_03_Pcalcareum_Population_Structure.R): `SNP_03_Pcalcareum_Population_Structure.R`
- [L. corallioides structure](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_04_Lcorallioides_Population_Structure.R): `SNP_04_Lcorallioides_Population_Structure.R`
- [Fst analysis](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/SNP_05_Fst.R): `SNP_05_Fst.R`
- [SNP analysis outputs](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/outputs): `outputs`

### Climate adaptation

- [Climate and site data](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/data/environmental_data): `data/environmental_data`
- [Climate data processing](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/GEA_01_Climate_Data.R): `GEA_01_Climate_Data.R`
- [P. calcareum RDA offset](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/GEA_02_Pcalcareum_RDA_Offset.R): `GEA_02_Pcalcareum_RDA_Offset.R`
- [L. corallioides RDA offset](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/GEA_03_Lcorallioides_RDA_Offset.R): `GEA_03_Lcorallioides_RDA_Offset.R`

### Supporting analyses

- [Kraken microbiota data](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/data/kraken_results): `data/kraken_results`
- [Microbiota analysis](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/Microbiota_Analysis.R): `Microbiota_Analysis.R`
- [DNA barcodes](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/tree/main/data/DNA_barcoding): `data/DNA_barcoding`
- [Species tree](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/data/astral_results/busco_genes_ASTRAL_spp.tree): `data/astral_results/busco_genes_ASTRAL_spp.tree`
- [Figure generation](https://github.com/tom-jenkins/maerl_whole_genome_resequencing/blob/main/Figure_01.R): `Figure_01.R`

### Other components

- **Researcher**

## Connections

- Researcher → SNP quality control: runs analysis
- Researcher → Allele balance and ploidy: runs analysis
- Researcher → P. calcareum structure: runs analysis
- Researcher → L. corallioides structure: runs analysis
- Researcher → Fst analysis: runs analysis
- Researcher → Climate data processing: runs analysis
- Researcher → P. calcareum RDA offset: runs analysis
- Researcher → L. corallioides RDA offset: runs analysis
- Researcher → Microbiota analysis: runs analysis
- Researcher → Figure generation: runs analysis
- Climate data processing → Climate and site data: processes data
- Microbiota analysis → Kraken microbiota data: analyzes data