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afterqc website  

AfterQC Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats

Environment Modules

Run module spider afterqc to find out what environment modules are available for this application.

System Variables

  • HPC_AFTERQC_DIR - installation directory
  • HPC_AFTERQC_BIN - executable directory
  • HPC_AFTERQC_MAN - manual directory


If you publish research that uses afterqc you have to cite it as follows:

Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu and Jia Gu. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics 2017 18(Suppl 3):80