bacteria_viability

QIIME2 and R code for "DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta"

All raw data from the Illumina MiSeq run are available under NCBI BioProject ID PRJNA971764.

Files provided

1. Bacteria_Viability_Metarbarcoding.pdf: This outlines the QIIME2 code for processing all raw data files, generating the precursor files for data analysis in R. Users unfamiliar with QIIME2 can follow along with a tutorial I designed in partnership with Melbourne Bioinformatics

2. Data files used for analysis in R:

   a. metadata.tsv

   b. taxonomy.txt

   c. asv.txt

   d. tree.nwk

3. R code files:

   a. 1_import_data.R

   b. 2_decontam.R

   c. Acropora loripes.R

   d. Acropora millepora.R

   e. Acropora tenuis.R (note that this is for the A. kenti samples)

   f. Platygyra daedalea.R

   g. Pocillopora acuta.R

   h. Porites lutea.R

Should you have any questions or find a mistake, please contact Ashley Dungan at adungan31@gmail.com

You are welcome to use this code for any of your research - please reference this GitHub page if you do.