FastX Toolkit

FastX Toolkit is a collection of command line tools for short-reads file processing.

Available tools

  • FASTQ-to-FASTA converter;
  • FASTQ Information;
  • FASTQ/A Trimmer;
  • FASTQ/A Reverse-Complement;
  • FASTQ Quality Filter;
  • Many others…



sudo apt-get install fastx-toolkit


#convert FASTq to FASTA file
fastq_to_fasta -i file.fq -o filename.fasta

#calculate statistics for original data
fastx_quality_stats -i file.fq -o file.stats   #calculates -i file.stats -o file.png  #creates graphs

fastx_trimmer -f 1 -l 100 -i file.fq -o file.trimmed   

#[-f] = First base to keep. Default is 1 (=first base).
#[-l] = Last base to keep. Default is entire read.

#filter low quality score reads
fastq_quality_filter -q 20 -p 80 -i file.trimmed -o file.filtered

#[-q] = Minimum quality score to keep
#[-p] = Minimum percent of bases that must have [-q] quality

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