10 Resources:

Here are some resources that are helpful for running the analysis

10.1 Data in this analysis

Download to data from this analysis Github repo (See Bosch et al. [2])

10.2 Other resources

This analysis uses various software and tools all made available through the Graham cluster. These are some of the coding languages, tools and software we used in this analysis:

R/RStudio: R and RStudio are utilized for generating plots using the QIIME2R and Phyloseq packages. R is a statistical programming language widely employed in data analysis and visualization, while RStudio provides an integrated development environment (IDE) for working with R.

FastQC: FASTQC is a quality control tool used to assess the quality of sequencing data.

MultiQC: MultiQC is a tool that aggregates results from multiple bioinformatics analyses into a single, comprehensive report to evaluate and summarize quality control metrics.

QIIME2: QIIME2 is a powerful microbiome analysis platform used extensively in this analysis. It provides a comprehensive suite of tools for processing, analyzing, and visualizing microbiome data.

Near the end of this analysis, we export the final files from the cluster to a local computer (your computer) and use two different R packages locally to run a few other analyses and plot a taxonomic heatmap and barplot. While QIIME2 does offer heatmap/barplot capabilities, the aesthetic features are more limited than QIIME2R and Phyloseq. To use QIIME2R and Phyloseq on your local computer, make sure you have R and RStudio installed.

QIIME2R: QIIME2R is an R package that enables integration between QIIME2 and R. It allows importing QIIME2 artifacts and visualizing data within the R environment, and offers further data exploration beyond what QIIME2 currently offers.

Phyloseq: Phyloseq is an R package that works seamlessly with QIIME2 data and provides a flexible framework for modifying and visualizing data.

Some Digital Alliance pages that are worth checking out:

 

Github: johannabosch