Quality Control Scripts

Scripts for running Quality Control on NGS data in fastq.gz format

Current tools:

• FastQC: quality metrics for fastq
• Kraken: metagenomic analysis, useful for detecting possible contaminants
• Krona: create interactive pie chart from Kraken output

These tools must be installed and configured for your system.

This script is designed to work on the NYU HPC system by submitting jobs to the SGE cluster, but it can also be modified to simply run in the current session.

In the current implementation, the script will search the input_dir for all *.fastq.gz files, and run the selected script on them. A subdirectory for each input file will be create in the output_dir, where program output will be placed.

Usage:

run_qc.sh /path/to/output_dir /path/to/input_dir FastQC_Kraken_Krona.sh

Sample output

FastQC ouptput

Krona plot snapshot