RNA-Seq has become one of the most widely used applications based on next-generation sequencing (NGS) technology.However,raw RNA-Seq data may have various quality issues,which can significantly distort analytical results and lead to erroneous conclusions.Therefore,the raw data must be subjected to quality control procedures before downstream analysis.However,the existing QC tools for RNA-Seq data have various limitations like incompletefunctions,long running time and poor usability.Here we report RNA-QC-Chain,a comprehensive,fast and easy-to-use QC pipeline for RNA-Seq data,which involves three steps: (1) sequencing-quality assessment and trimming;(2)internal and external contamination filtering;(3) alignment statistics (such as read number,alignment coverage,sequencing depth and pair-end read mapping statistics).It also has several unique features that are not available in other RNA data QC tools,such as sequence trimming,automatic rRNA filtration and contaminating species identification,The three QC steps can run either sequentially or independently,enabling it a comprehensive package with high flexibility.Moreover,parallel computing is applied in most of the QC procedures,making it runs fast.The performance of RNA-QC-Chain has been evaluated with a RNA-Seq dataset of an algae species Nannochloropsis.Comparison of RNA-QC-Chain with other QC tools showed that it is superior in both function versatility and processing speed.