How tom-jenkins/maerl_whole_genome_resequencing works
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 Climate data processing · Microbiota_Analysis.R Microbiota analysis · SNP_01_QC_Filter.R SNP quality control · SNP_02_Allele_Balance_Ploidy.R Allele balance and ploidy
Components 16
Population genomics
- SNP quality control
SNP_01_QC_Filter.R - Allele balance and ploidy
SNP_02_Allele_Balance_Ploidy.R - P. calcareum structure
SNP_03_Pcalcareum_Population_Structure.R - L. corallioides structure
SNP_04_Lcorallioides_Population_Structure.R - Fst analysis
SNP_05_Fst.R - SNP analysis outputs
outputs
Climate adaptation
- Climate and site data
data/environmental_data - Climate data processing
GEA_01_Climate_Data.R - P. calcareum RDA offset
GEA_02_Pcalcareum_RDA_Offset.R - L. corallioides RDA offset
GEA_03_Lcorallioides_RDA_Offset.R
Supporting analyses
- Kraken microbiota data
data/kraken_results - Microbiota analysis
Microbiota_Analysis.R - DNA barcodes
data/DNA_barcoding - Species tree
data/astral_results/busco_genes_ASTRAL_spp.tree - Figure generation
Figure_01.R
Other components
- Researcher
Connections 12
- 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