This repository contains the microbiome data analysis for the manuscript
Thanissery R, McLaren MR, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston JA, Jacob M, Callahan BJ, Theriot CM. 2019. Characterization of C. difficile strains isolated from companion animals and the associated changes in the host fecal microbiota. bioRxiv 822577. doi:10.1101/822577
The raw sequence reads are available at
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562547. The results of
bioinformatic analysis of the raw reads with DADA2, including taxonomy
assignment against Silva v132 using DADA2's assignTaxonomy() and
addSpecies() functions are in results/dada2, and as a
phyloseq object in results/ps.Rds.
The results/ folder also includes plain-text (.csv format) tables mapping ASV names to their amplicon sequence and taxonomy. These tables can be viewed directly in a web browser by clicking the below links.
- Table of all ASV sequences
- Table of select ASV sequences (all Clostridiodes ASVs, all Clostridium hiranonis ASVs, and ASVs shown in Figure 3)
- Table of ASV sequences explicitly mentioned in the manuscript (Excludes low-prevalence C. hiranonis ASVs)
All bioinformatic and statistical analyses are contained in R-markdown documents in analysis/. A description of these files and links to rendered versions showing all numerical output and figures is given in analysis/README.md.