Biogeography of reef water microbes from within reef to global scales

Code used for analyses, figure generation, and formatting of the manuscript.

Sequence quality control

Raw sequence reads for the primary analysis were processed using the DADA2 workflow optimized for iSeq data found in this repository, using parameters detailed in the paper. Output from DADA2 are found in the folder 'output'. For the secondary analysis, the MiSeq version found here was used and output can be found in 'SMeta/output'.

Reads were then filtered and preprocessed using 'preprocessing.R' and 'preprocessing_SMeta.R' and deposited in the respective 'processed' folder.

Data analysis

All code for analyses, figures, and tables generated for this paper (and some that didn't make it) can be found in the 'code' folder with descriptive filenames and a short descriptive header indicating the number of the figure it generates.

Manuscript

The manuscript for this paper was written in RMarkdown in the file 'Spatial_manuscript.Rmd' and exported into Word format. To compile the manuscript after running all scripts in 'code', run the following in R:

library(rmarkdown)
library(bookdown)
library(tools)
render("Spatial_manuscript.Rmd", output_format="word_document2")