Objective To investigate the quality control of the next-generation sequencing data by analyzing some im-portant problems with quality control in order to provide high-quality data for the downstream data analysis .Method The software Fastq_clean was developed to clean the data and to statistically analyze the quality of the data.Result Using a Chrysanthemum transcriptome dataset , the function of the Fastq_clean software was illustrated .Conclusion Based on the Bioconducter package , the Fastq_clean software can accurately remove low quality nucleotides and Ns , adapter contamina-tion, possible rRNA and virus contamination .Moreover, it can keep the largest possible amount of high-quality data reads.