Genomic sequence analysis starts from a sequence with poor quality such as mis-orientation, incorrect location or contig order can hardly produce fruitful results in final assays. Unfortunately, more than often the circumstance is not found early enough until a lot of time and effort has been invested. To alleviate this situation, we have developed QualiSeq, a web application with a friendly interface providing information on sequence quality of a genomic region so that researchers can easily download much more reliable sequences for further analysis and assay design.