Q&A 2 How do you obtain example microbiome sequencing data for analysis?

2.1 Explanation

Before performing any analysis, you need access to microbiome sequencing data. This data typically comes in the form of FASTQ files (either single-end or paired-end), which contain raw reads from amplicon sequencing.

There are several sources for publicly available datasets: - QIIME2 Tutorials: Include curated sample data for testing pipelines - NCBI SRA / EBI ENA: Provide raw sequencing data from published studies - Qiita: A microbiome database for submitting and reusing 16S/18S/ITS data - Mock communities: Simulated or synthetic datasets used to benchmark tools

This example uses the classic Moving Pictures tutorial dataset from QIIME2.

2.2 Shell Code

# Download paired-end FASTQ data from QIIME2 tutorial
wget https://data.qiime2.org/2024.2/tutorials/moving-pictures/emp-paired-end-sequences/barcodes.fastq.gz
wget https://data.qiime2.org/2024.2/tutorials/moving-pictures/emp-paired-end-sequences/forward.fastq.gz
wget https://data.qiime2.org/2024.2/tutorials/moving-pictures/emp-paired-end-sequences/reverse.fastq.gz

2.3 Python Note

# Although QIIME2 is Python-based, raw sequencing data is usually downloaded externally.
# Python/QIIME2 will be used later to import and process these FASTQ files.

2.4 R Note

# Most raw sequencing workflows do not begin in R. However, after generating feature tables
# from tools like QIIME2 or mothur, R will be used for downstream analysis and visualization.