This repository contains a collection of Bash scripts developed for performing QIIME2-based analysis on gut-microbial data. The scripts automate various stages of the analysis pipeline, including data acquisition, quality control, sequence processing, and taxonomic classification.
The aim of this project is to provide a streamlined and automated approach to analyzing microbial community data using QIIME2, focusing on the gut microbiome. The scripts included in this repository facilitate the following key tasks:
- Data Download: Automated downloading of datasets using
wget, with options to make the datasets executable. - Quality Control: Execution of FastQC and MultiQC for assessing the quality of raw sequence data.
- Sequence Counting: Generation of CSV files that count the number of sequences per sample in FASTQ format.
- Sample Filtering: Removal of low-quality samples based on sequence count thresholds.
- Sequence Processing: Execution of
fastpfor processing and quality filtering of sequence data. - QIIME2 Analysis: A series of QIIME2 commands for importing data, conducting sequence quality control, generating feature tables, performing taxonomic classification, and visualizing results.
- Bash Automation: Scripts are designed to automate repetitive tasks, reducing the potential for errors and saving time.
- Comprehensive Workflow: Covers all major steps from raw data acquisition to taxonomic analysis and visualization.
- Customizable: Parameters and file paths can be easily adjusted to fit specific datasets or research needs.
To use these scripts, ensure that the following tools are installed and properly configured on your system:
- Bash: The scripts are written in Bash and should be executed in a Unix-like environment.
- FastQC: For quality control of raw sequences.
- MultiQC: For aggregating results from FastQC and other tools.
- fastp: For fast and accurate sequence preprocessing.
- QIIME2: For comprehensive microbiome analysis.
Installation commands for these tools are provided in the respective script comments.
- Download the dataset using the provided script, and ensure it is executable.
- Run quality control checks on the raw sequence files using FastQC and MultiQC.
- Count sequences per sample and filter out low-quality samples.
- Process the sequences with
fastpto ensure high-quality data. - Execute the QIIME2 commands to perform taxonomic analysis and generate visualizations.
Each script is designed to be run independently, allowing you to tailor the workflow to your specific needs.