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Haverö metabarcoding study

Publication reference

This repository contains material supporting the following publication:

Harrison JP, Chronopoulou P-M, Salonen IS, Jilbert T, Koho KA. (2021) 16S and 18S rRNA gene metabarcoding provide congruent information on the responses of sediment communities to eutrophication. Frontiers in Marine Science 8:708716. doi: 10.3389/fmars.2021.708716

Repository contents

The contents include:

  • R scripts used for data analysis and package installations (/rscripts)
  • phyloseq objects including data processed in micca (/rdata)
  • environmental metadata (/envdata)
  • a Singularity definition file and software license file (/singularity)
  • output files generated by R scripts (/figures, /stats)

Descriptions of R scripts:

PCA.R Script for environmental metadata PCA

16S_singularity_datachecks.R and 18S_singularity_datachecks.R: Data analysis scripts for inspecting data pre-processing steps

16S_singularity.R and 18S_singularity.R: Data analysis scripts generating most output files

taxa_summary.R: Phyloseq supporting script, originally available here

imagestitch.R Script for combining and editing figure files

extra_RPackages.R Script for additional R package installations

Reproducing the R environment + analyses used

1. Clone the repository and move to the singularity folder

git clone https://github.com/jessepharrison/seili-metabarcoding.git
cd seili-metabarcoding/singularity

2. Build the Singularity container

This takes some time - grab yourself a coffee!

sudo singularity build seili.sif container.def

3. Install further R packages

Run the following still in the singularity folder:

singularity exec seili.sif \
Rscript --no-save ../rscripts/extra_RPackages.R

# note 1:
# the script will install the packages to the current working directory.
# the actual data analysis scripts add /singularity to libpaths.
# hence it's important to make sure you install everything to /singularity!

# note 2:
# the container is configured to use a MRAN snapshot from 2020-11-29.

4. Running analysis scripts

You can now move back to the repository root (path/to/seili-metabarcoding).

The scripts can be run non-interactively using Rscript, for example:

singularity exec singularity/seili.sif \
Rscript --no-save rscripts/PCA.R

The imagestitch.R script should be run last as it relies on figure files created by other scripts.

c) If wanting to work with RStudio:

unset XDG_RUNTIME_DIR
singularity exec singularity/seili.sif \
rstudio