Quality Control of NGS Data

Welcome to the NGS-QC web application. This tool allows you to upload FASTQ files and perform quality control analysis.

To get started, please upload your FASTQ file using the form below.

Description:

NGS-QC is a Bioinformatics tool to perform quality control analysis of next-generation sequencing (NGS) data. It is designed to work with FASTQ or gzipped files generated from different NGS platforms. The results are presented in a user-friendly format, allowing researchers to quickly assess the quality of their sequencing data. The tool provides a comprehensive analysis of the sequencing data as follows:

• FastQC: read quality scores, length distribution, GC content, and adapter contamination, etc.
• BWA/Minimap2: map the reads to a reference sequence (HXB2 or user provides). BWA is best for the short reads (e.g. Illumina). Minimap2 provides two options. Minimap2-sr works for the short reads, Minimap2-lr:hq is for the long reads (e.g. PacBio and Nanopore)
• SAMtools: calculate the read mapping stats such as number of mapped reads, mapping quality (MAPQ), read depth, breadth coverage and maximun base frequency across reference, etc.
• MultiQC: visualizion of the sequencing quality control analysis.

Contact:

For any questions, bugs and suggestions, please send email to CohnLabSupport@fredhutch.org and include a few sentences describing, briefly, the nature of your questions and include contact information.

© 2025 Fred Hutch Cancer Center. All rights reserved.