Re-evaluating the evidence for fecal microbiota transplantation "super-donors" in inflammatory bowel diseases

Author: Scott Olesen solesen@openbiome.org

Files

• README.md: This file
• donor-effects-env.txt: Conda environment file
• install-packages.R: R script that installs packages needed for analyses
• Snakefile: A Snakemake file with instructions for how to repeat the analyses
• 16S-common.snakefile: A Snakemake file with instructions for 16S rRNA data processing
• 16S-single.snakefile: 16S processing for single-ended reads (Goyal et al.)
• 16S-paired.snakefile: 16S processing for paired-ended reads (Jacob et al. and Kump et al.)
• costello/: Re-analysis of Costello et al.
• goyal/: Re-analysis of Goyal et al.
• jacob/: Re-analysis of Jacob et al.
• kump/: Re-analysis of Kump et al.
• moayyedi/: Re-analysis of Moayyedi et al.
• nishida/: Re-analysis of Nishida et al.
• nusbaum/: Re-analysis of Nusbaum et al.
• paramsothy/: Re-analysis of Paramsothy et al.
• pools/: Analysis of the 3 "pool stool" studies
• rossen/: Re-analysis of Rossen et al.
• utils.R: Utilities for R scripts
• uygun/: Re-analysis of Uygun et al.
• vaughn/: Re-analysis of Vaughn et al.

Goyal, Jacob, Kump, and Nusbaum have subfolders diversity-data/, which are the workspaces for the 16S Snakefiles. The alpha- and beta-diversity results are placed there.

Getting started

1. Install conda
2. Install the working environment (Qiime and Snakemake): conda create --name donor-effects --file env.txt
3. Install R packages using ./install-packages.R into that environment
4. Run snakemake in that environment