Quality Control of NGS Data

Quality Control of NGS Data

Next-generation sequencing (NGS) technologies generate vast amounts of genomic, transcriptomic, and epigenomic data, which necessitates rigorous quality control (QC) to ensure accuracy, reproducibility, and meaningful biological interpretation. This comprehensive course provides in-depth training on NGS data QC, including experimental design considerations, preprocessing, error detection, and optimization of sequencing workflows across diverse applications such as genomics, transcriptomics, epigenomics, and metagenomics. Participants begin with an introduction to NGS technologies, library preparation, sequencing platforms (Illumina, PacBio, Oxford Nanopore), and common sources of error including base calling, adapter contamination, PCR bias, and sequencing artifacts. The course emphasizes the importance of QC at each stage of the sequencing workflow, from raw data acquisition to downstream analysis. Core modules cover data preprocessing, including quality assessment using tools like FastQC, MultiQC, and Qualimap; trimming and filtering reads; removal of adapters and low-quality sequences; and detection of contaminant sequences. Participants gain hands-on experience with real datasets, learning to interpret QC reports, identify systematic errors, and make informed decisions on read retention or removal. Advanced topics include normalization methods, duplication assessment, alignment quality evaluation, error correction, and coverage assessment. Participants explore QC strategies for RNA-Seq, DNA-Seq, ChIP-Seq, ATAC-Seq, and single-cell sequencing, emphasizing platform-specific considerations and best practices. Integration with downstream bioinformatics pipelines is highlighted, including variant calling, differential expression analysis, genome assembly, and metagenomic profiling. Participants learn to implement reproducible workflows, automate QC processes, and document decisions to ensure transparency and reproducibility. Case studies demonstrate the impact of QC on experimental outcomes, highlighting the identification of sequencing artifacts, batch effects, and contamination. Emphasis is placed on the integration of QC metrics into experimental reporting and compliance with community standards. By the end of this course, participants will be able to perform comprehensive QC of NGS datasets, preprocess reads effectively, detect and correct errors, optimize sequencing workflows for diverse applications, integrate QC into bioinformatics pipelines, and communicate findings clearly. This training equips bioinformaticians, genomics researchers, and computational biologists with essential skills to ensure high-quality, reliable, and reproducible NGS data analyses.

Syllabus

• Module 1: Introduction to NGS Technologies and Platforms
• Module 2: Sources of Error in Sequencing and Experimental Design
• Module 3: Quality Assessment Tools (FastQC, MultiQC, Qualimap)
• Module 4: Trimming, Filtering, and Adapter Removal
• Module 5: Error Detection and Correction
• Module 6: Duplication and Coverage Assessment
• Module 7: QC for RNA-Seq, DNA-Seq, ChIP-Seq, ATAC-Seq
• Module 8: QC for Single-Cell Sequencing
• Module 9: Integration with Downstream Pipelines
• Module 10: Case Studies and Best Practices in NGS QC

Prerequisites

Basic knowledge of molecular biology, genomics, and bioinformatics; familiarity with sequencing data and Linux command-line

Learning Outcomes

Assess quality of raw NGS reads; Trim, filter, and remove low-quality sequences; Detect and correct sequencing errors; Evaluate alignment and coverage; Implement QC for various sequencing platforms; Integrate QC into downstream pipelines and reproducible workflows; Communicate QC findings effectively

Certificate

Participants who successfully complete the training program will be awarded an official Certificate of Completion issued by Helix Institute for Medical & Biological Sciences LLC (USA).
The certificate confirms that the participant has attended and fulfilled the academic and practical requirements of the course, including lectures, workshops, assignments, and assessments, where applicable.
Each certificate includes:

• Full name of the participant
• Duration and total instructional hours
• Date of completion
• Title of the training program
• Official signature of the authorized representative of Helix Institute
• Institutional logo and identification number (Certificate ID)
• Verification reference for authenticity

Certificates issued by Helix Institute are designed to support professional development, academic portfolios, and continuing education records. Participants may use the certificate as evidence of specialized training in biomedical and life sciences disciplines.
For selected programs, certificates may also be issued in collaboration with partner institutions, universities, or scientific organizations when applicable.
Helix Institute maintains records of issued certificates to ensure verification and transparency. Employers, academic institutions, and professional organizations may request confirmation of certificate authenticity through official communication with the Institute.
Certificates are delivered electronically in secure digital format upon successful completion of the program. Printed certificates may be issued upon request.