Max Planck Institute for Developmental Biology

Talia Karasov

This repository contains scripts related to the controlled metagenomic infections performed in 2018 and 2019 and described here: https://www.biorxiv.org/content/10.1101/828814v1

The study analyzes the ratio of microbial reads to plant reads in Arabidopsis thaliana populations in Sweden and Germany to determine which microbes reach high relative abundances. To determine the relationship between load and disease we then compare the load measurements to measurements of disease progression from the laboratory.

DEPENDENCIES

Read Mapping of Plant and Metagenome

• python3
• bwa (version 0.7.17-r1188)
• picard (version 2.17.3)
• samtools (version 1.6-19-g1c03df6(using htslib 1.6-53-ge539b32)
• centrifuge (version 1.0.4)

Analysis of metagenomes post-centrifuge

• R (version 3.5.3)
• Major R packages
  • vegan (version 2.5.5)

SCRIPTS

The general pipeline for assessing metagenomic load can be found in this repository though there is a lot of unrelated code here.

• https://github.com/tkarasov/metagenomics_pipeline

The manuscript used the pipeline for centrifuge.

• Script to run the whole pipeline

Script-by-Script rundown of the Pipeline to build the metagenome table

• Script to remove plant reads from the metagenomes
• Script to run centrifuge
• Script to make kreport
• Script to recalibrate kreport
• Script to subsample centrifuge output to look at normalized data
• Script to separate fungal, oomycete and bacterial reads output from centrfiuge
• The actual analysis script to recalibrate the output from centrifuge to genome coverage

Scripts for Figure generation and statistics

• [Folder for scripts for figure generation] (https://github.com/tkarasov/controlled_metagenomics/tree/master/scripts/keep_used_in_publication)
• Figure 1: Stacked barplots
• Figure 2: Diversity measurements
• Figure 2: PCoA
• Figure 3: Lab comparisons (DC3000)
• Figure 3: Lab comparisons (HpA)
• Deseq: Variance stabilization between Sweden and Germany

DATA

For metagenome classification and normalization

• The ncbi taxonomy tree used for family-wise calculation of load
• The ncbi genome size file

Field trials

• Swedish metagenome table for oomycete:
  • Bacteria
  • Oomycetes
  • Fungi
• German metagenome table
  • Bacteria
  • Oomycetes
  • Fungi

Laboratory infection trials

• Pst DC3000 infections
  • Bacteria
  • Oomycetes
  • Fungi
• Hpa infections
  • Bacteria
  • Oomycetes
  • Fungi