Cochineal 16s

A 16S data analysis of the cochineal metagenome.

1 Directory Structure

cochineal_16s
  ├── reports -> R Analysis Notebooks 
  ├── data -> Raw data, metadata and processed results
  ├── docs -> Documentation
  └── pipes -> Scripts to reproduce analysis from scratch
  • The analysis notebooks are rendered in HTML and available here.

2 Reproducing the analysis

2.1 Environment setup

  1. First, clone the repository:
https://github.com/dalmolingroup/cochineal_16s.git

Then, from the root of the repository, you can run the rest of the analysis in the steps outlined in this document.

  1. Install nextflow

3 Running the analysis

  1. Process the 16S data:
bash pipes/run_ampliseq.sh
  1. Copy over useful results from the ampliseq execution:
bash pipes/copy_report.sh
  1. Render quarto notebooks
quarto render