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AfterQC

Description

afterqc website

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 0.9.7 or newer formats

Environment Modules

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

Environment Variables

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

Citation

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

Chen, S., Huang, T., Zhou, Y. et al. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics 18 (Suppl 3), 80 (2017). https://doi.org/10.1186/s12859-017-1469-3

Categories

phylogenetics