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fastq-tools website  

This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.

Required Modules


  • fastq-tools

System Variables

  • HPC_{{#uppercase:fastq-tools}}_DIR - installation directory

Additional Information

  • fastq-sort : sort fastq entries by various keys
  • fastq-grep : match sequences against regular expressions
  • fastq-kmers : count k-mer occurrences
  • fastq-match : (smith-waterman) local sequence alignment
  • fastq-qual : tabulate quality scores
  • fastq-sample : randomly sample reads, with or without replacement
  • fastq-uniq : count duplicate reads
  • fastq-qualadj : adjust quality scores by a fixed offset