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Overview

This GitHub repository contains a Jupyter notebook for analyzing the taxonomy of reads from the microbiome of the Georiga Aquarium Ocean Voyager exhibit using QIIME 2, a bioinformatics platform for analyzing microbial communities.

Requirements

To use the notebook in this repository, you will need

• A QIIME 2 conda environment
• Git Large File Storage (LFS)

Data

The dataset used is a 14-month timeseries of 16S sequencing data of the microbiome from Georgia Aquarium's Ocean Voyager (OV) aquarium exhibit. FASTQ sequences (SRA accession PRJNA417313, original publication) were downloaded from the NCBI Sequence Read Archive (SRA) after installing the SRA toolkit and Entrez Direct and running the command

esearch -db sra -query PRJNA417313  | efetch | cut -d ',' -f 1 | grep SRR | xargs fastq-dump --split-files

Data was downloaded to a folder named "ov_data" in the repository root directory. These FASTQ files are untracked due to size.

Folder Structure

• qiime_analysis: contains qiime_analysis.ipynb analysis notebook and related output files (.qza, .qzv) from QIIME 2

Usage

To generate the taxonomy bar plot using QIIME 2:

• Install Git LFS to download "qiime_analysis/paired-end-demux.qza"
• Install QIIME 2 locally
• Activate the QIIME 2 conda environment using the environment’s name:: conda activate qiime2-2023.2
• Launch jupyter notebook or jupyer lab
• Run the qiime_analysis.ipynb Jupyter notebook