[WIP] Document workflow from raw data to analyses

[ropolomx]

Work in progress: adding information and designing workflow for processing data from raw reads to downstream analyses

Should include:

• [ ] Bioinformatics workflow (i.e. Snakemake)

• [ ] Exploratory data analysis with Pavian

• Exclude Apis mellifera

• Include Bacteria

• Include some eukaryotes: Nosema, trypanosomes - Crithidia mellificae, Varroa

• [ ] Exploratory data analysis with Krona (multiple samples in one) *Look into implementation of Krona steps in nf-core/mag

• [ ] Downstream R analyses

  1. Exploratory data analysis: barplots of the 5 core microbiome genera
  2. Cumulative Sum Scaling normalization with cumNorm function
  3. Alpha diversity on both unnormalized and normalized data and visualization, and statistical analyses
  4. Beta diversity (ordination) with both unnormalized and normalized data, and statistical analyses
  5. Differential abundance
  6. Modularization: https://cran.r-project.org/web/packages/modules/vignettes/modulesAsFiles.html