coprolite_analysis

This repository contains the scripts and results of the analyses on NGS data from kuri palaeofaeces

02-scripts contains all the scripts, divided into two parts conform with my PhD thesis: one kuri genome analysis part, and another metagenomic part

• genome_analysis/
  
  • Rstudio_scripts/
    
  • bash_scripts/
    
  • python_scripts/
    
• metagenome_analysis/
  
  • Rstudio_scripts/
    
  • bash_scripts/
    
  • python_scripts/
    

05-results are orderd by the type of analysis, including

• bacterial_mapping/
  
  • all_bacteria/
    
  • fish_spoilers/
    
  • fusobacterium_perfoetens/
    
• contammix/
  
• diet_mapping/
  
  • COI_region/
    
  • mitochondrion/
    
  • plants/
    
• genotyping/
  
• kinship/
  
• kraken/
  
  • bracken_reports/
    
  • kracken_reports/
    
• maaslin_kuri_CLR_figures/
  
• mapdamage/
  
  • fragmisincorporation_plots/
    
  • frequencies/
    
  • ength_plots/
    
• metaphlan/
  
  • reports_negatives/
    
  • reports_over50bp/
    
  • reports_under50bp/
    
• mtDNA_results/
  
  • genotyping/
    
  • mapdamge/
    
  • mtDNA_fastas/
• RStudio/
  
  • metagenomic/
    
  • modern_mapping/
    
  • nucleotide_diversity/
    
  • PCA/
    
  • trees/
    
• sourcepredict/
  
  • filtered_reports/