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fqtools website  

fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are supported. See below for a full list of the subcommands available and a brief description of their purpose. Most of the individual subcommands will take either a single file or a pair of files as input. If no input file is specified, fqtools will attempt to read data from stdin. In this case, it is advisabe to specify the format of the data provided. For subcommands that generate FASTQ data, either a single file or a pair of files will be generated. If no -o argument is provided, single files will be writted to stdout.

Required Modules


  • gcc/5.2.0
  • fqtools

System Variables

  • HPC_FQTOOLS_DIR - installation directory


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

Droop, A. P. (2016). fqtools: An efficient software suite for modern FASTQ file manipulation. Bioinformatics (Oxford, England).