Metagenomic Analysis Pipeline

Table of Contents

• Description
• Installation
• Dependencies
• Usage
  • Parameters
• Example
• Output
• Contributing

Description

This repository contains a Bash script for automating various steps in a metagenomic analysis pipeline. The script merges .fq files, performs adapter trimming, and classifies reads using Kraken.

Installation

Clone this repository to your local machine.

git clone https://github.com/Zubair2021/metagenome_analysis.git

Dependencies

Software

1. Bash: Make sure you have Bash shell installed on your system.
2. Kraken2: Download and install from Kraken2 GitHub Repository.
3. Bracken: Download and install from Bracken GitHub Repository.

You can typically install Kraken2 and Bracken using the following commands:

# For Kraken2
git clone https://github.com/DerrickWood/kraken2.git
cd kraken2
./install_kraken2.sh $PWD

# For Bracken
git clone https://github.com/jenniferlu717/Bracken.git
cd Bracken
./install_bracken.sh

Database

1. Kraken2 Database: You can build a Kraken2 database following the instructions here.

   kraken2-build --standard --threads 12 --db $KRAKEN_DB_NAME

2. Bracken Database: After building the Kraken2 database, you can build the Bracken database.

   bracken-build -d $KRAKEN_DB_NAME -k 35 -l 150

Note: Replace $KRAKEN_DB_NAME with the name you wish to give to your Kraken2 database.

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Adapter sequences in a .fa file

Usage

Parameters

• BASE_DIR: The base directory containing nested folders with .fq files.
• TARGET_DIR: Target directory to store merged .fq files and output files.
• TRUSEQ_ADAPTERS: Path to the adapter sequences in .fa format.
• KRAKEN_DB: Path to the Kraken database.

To run the script, navigate to the directory containing the script and execute:

bash metagenome_full_pipeline.sh

Example

BASE_DIR="/path/to/raw_data"
TARGET_DIR="/path/to/output"
TRUSEQ_ADAPTERS="/path/to/adapters.fa"
KRAKEN_DB="/path/to/krakenDB"

Output

The output directory will contain the following:

• Merged .fq files
• Trimmed .fq files
• Kraken classification reports

Contributing

If you wish to contribute, please open an issue or submit a pull request.

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