AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. - Shifu Chen; Tanxiao Huang; Yanqing Zhou; Yue Han; Mingyan Xu; Jia Gu (BMC Bioinform., 2017)

MutScan: fast detection and visualization of target mutations by scanning FASTQ data. - Shifu Chen; Tanxiao Huang; Tiexiang Wen; Hong Li; Mingyan Xu; Jia Gu (BMC Bioinform., 2018)

Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data. - Shifu Chen; Yanqing Zhou; Yaru Chen; Tanxiao Huang; Wenting Liao; Yun Xu; Zhicheng Li 001; Jia Gu (BMC Bioinform., 2019)