kauri-soil-comparative

This repository contains all the code used in Chapter 2 - Comparative amplicon and shotgun metagenome profiling of soil microbial communities in kauri forests affected by Phytophthora agathidicida.

There is an associated wiki page that runs through the data analysis workflow for this chapter.

The repository is structured as follows:

• amplicon-data contains the scrips used to run DADA2 and analyse the amplicon reads.
  • DADA2 processing scripts are in 00_16S-amplicon-scripts and 00_ITS-amplicon-scripts.
  • Scripts used to analyse the taxonomic composition and functional potential of the communities are in 01_taxonomy_scripts and 02_function-picrust2-scripts.
• metagenome-data contains the scripts used to run QC on the shotgun metagenome reads as well as taxonomically and functionally annotating the reads.
  • 00_quality_control contains scripts for trimming and filtering reads.
  • 01_taxonomy_scripts contains scripts for running Kraken2 and Bracken for taxonomic classification of reads and the associated R scripts for analysis.
  • 02_function_scipts contains scripts for further cleaning of reads, assembly using MEGAHIT, gene prediction using Prodigal, annotation using eggNOG, and various other processing scripts.
• R-combined-scripts contains the scripts used to compare the outputs from amplicon and shotgun sequencing.
• misc-scripts contains several different scripts, including parsing KEGG information, rarefaction curve generation, creating bubble pie charts, and comparing PA detection methods.