How X-ray CT scanning affects microbial communities in sediments
Authors: Erica Ewton, Scott Klasek, Erin Peck, Jason Wiest, and Frederick Colwell
Publication: In press in Frontiers in Microbiology.
Reproducible workflow:
This repo shows codes for analyzing sediment microbial community responses to X-ray CT scanning.
Sequence data are 16S rRNA V4 hypervariable regions are available on NCBI.
For code showing the processing of ASVs from raw fastq sequences and the generation of phyloseq objects, see sequence processing.
For code showing analysis of microbial community data, see sequence analysis. If you're not interested in processing these sequences and want to skip to the analysis, you can begin with the phyloseq object ps4, which has been removed of unwanted taxa, decontaminated, and pruned of samples with very poor read depth.