A fast, accurate and holistic NGS data quality-control method. The tool synergeticly comprised of user-friendly tools for (1) quality assessment and trimming of raw reads using Parallel-QC, a fast read processing tool; (2) identification, quantification and filtration of unknown contamination to get high-quality clean reads. QC-Chain was optimized based on parallel computation, so the processing speed is significantly higher than other QC methods. Experiments on simulated and real NGS data have shown that reads with low sequencing quality could be identified and filtered. Possible contaminating sources could be identified and quantified de novo, accurately and quickly. Comparison between raw reads and processed reads also showed that subsequent analyses (genome assembly, gene prediction, gene annotation, etc.) results based on processed reads improved significantly in completeness and accuracy. As regard to processing speed, QC-Chain achieves 7-8 time speed-up based on parallel computation as compared to traditional methods.