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README.md

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Lake bacterial assemblage composition is sensitive to biological disturbance caused by an invasive filter feeder.

Authors: Vincent J. Denef, Hunter J. Carrick, Joann Cavaletto, Edna Chiang, Thomas H. Johengen, Henry A. Vanderploeg

Under review

This is the repository for the manuscript "Lake bacterial assemblage composition is sensitive to biological disturbance caused by an invasive filter feeder." written by Vincent J. Denef, Hunter J. Carrick, Joann Cavaletto, Edna Chiang, Thomas H. Johengen, and Henry A. Vanderploeg. The raw data can be obtained from the Sequence Read Archive at NCBI under BioProject PRJNA385848

Information about this repository:

Original fastq files:

The original Fastq files were submitted to the NCBI sequence read archive under BioProject PRJNA385848

Code Files:
QMexpall.Rmd includes all of the sequence data analysis!
This repo relies on functions in miseqR.R available on the MicrobeMiseq github on the DenefLab github page.
The folder DAPI contain additional input data and analyses for the DAPI count-based (Aug 2014 experiment) bacterial abundance analyses.
Directories/Directory Set up:
  1. Input_data: Includes the raw output files from the mothur pipline and the raw environmental data collected for the project. Including:
  2. DAPI Includes the detailed input data and data anlyses for the DAPI counts
  3. Figures: A home for all the figures created in the QMexpall.Rmd file.
    • This is where all the figures will be outputted.

Note: This project is under the GNU general public License.