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Analysis bash scripts, processed data files, and R scripts for Nutrient Enrichment Affects Mechanisms of Nitrogen Cycling in Oyster Microbiomes

Code written by Rebecca Stevick, URI-GSO (contact: rjstevick (at) gmail.com)

Collaborators: Ashley P. Hamilton, Serena Moseman-Valtierra, Anton F. Post, Marta Gomez-Chiarri

Study of farmed oysters and their associated nitrogen cycling in Point Judith Pond, RI.
The focus of this repository is analyses of bacterial 16S rRNA amplicon and microbial metatranscriptome data. Additional data and analyses from this study are in other repos TBD.

This repository contains the scripts, processed sequencing data, and the R script files to reproduce the figures in the manuscript. The raw sequences generated for this study can be found in the NCBI Short Read Archive under BioProject no. PRJNA599137. The corresponding accession numbers for each sample are detailed in PRJNA599137_NCBI_16Smetatrans.xlsx. This file also includes file names and general metadata for each 16S rRNA amplicon or metatranscriptomic sample.

To cite this work:

Stevick, R. J. (2019). Oyster-Associated Microbial Community Dynamics (Doctoral dissertation, University of Rhode Island).

Contents

EnvironmentalAnalysis

Envrionmental monitoring data and gas measurements - by Ashley Hamilton

  • mapping

16SampliconAnalysis

QIIME2 analysis of the 16S rRNA amplicon data

  • metadata
  • scripts
  • qiime2output
  • figures

MetatranscriptomeAnalysis

Functional analysis of the metatranscriptomic data

  • metadata
  • scripts
  • output
  • figures