10-Resources.Rmd

# **Resources:**

Here are some resources that are helpful for running the analysis

## **Data in this analysis**

Download to data from this analysis [Github repo](https://github.com/johannabosch/QIIME2_for_Graham/upload/main)
(See Bosch et al. **[2]**)

* To download the metadata files: https://github.com/johannabosch/QIIME2_for_Graham/tree/main/metadata

* To download the 2 rawdata files: https://drive.google.com/drive/folders/1mwfqLjyuLIpHO0KuhRAuxgYXjnbp1iQH?usp=sharing

## **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](https://www.r-project.org/):** 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](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/):** FASTQC is a quality control tool used to assess the quality of sequencing data.

> **[MultiQC](https://multiqc.info/):** MultiQC is a tool that aggregates results from multiple bioinformatics analyses into a single, comprehensive report to evaluate and summarize quality control metrics. 

> **[QIIME2](https://qiime2.org/):** 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](https://rstudio-education.github.io/hopr/starting.html) installed.

> [**QIIME2R**](https://github.com/jbisanz/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**](https://joey711.github.io/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:

* Storing data on the cluster
https://docs.alliancecan.ca/wiki/Storage_and_file_management#Best_practices

* Using Apptainer on a cluster: https://docs.alliancecan.ca/wiki/Apptainer

* Using QIIME2 on a cluster: https://docs.alliancecan.ca/wiki/QIIME


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<p style="text-align: center;">Github: [johannabosch](https://github.com/johannabosch) </a></p>
<p style="text-align: center;"><span style="color: #808080;"><em>yohannabosch@gmail.com</em></span></p>

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