FASTX-Toolkit pipeline

FASTX-Toolkit specifications


Unique identifier OMICS_01045
Name FASTX-Toolkit
Alternative name FastX toolkit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Output format FASTA, FASTQ
Operating system Unix/Linux
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
Maintained Yes


  • FASTQ-to-FASTA converter
  • FASTQ Information
  • FASTQ/A Collapser
  • FASTQ/A Trimmer
  • FASTQ/A Renamer
  • FASTQ/A Clipper
  • FASTQ/A Reverse-Complement
  • FASTQ/A Barcode splitter
  • FASTA Formatter
  • FASTA Nucleotide Changer
  • FASTQ Quality Filter
  • FASTQ Quality Trimmer
  • FASTQ Masker



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FASTX-Toolkit citations

PMCID: 5954061

[…] by the centre for applied genomics (tcag) at the hospital for sick children (toronto, on). the fastq files were trimmed based on a phred quality score >20 and read lengths >30 using the fastx toolkit (version 0.0.14), and the trimmed reads were mapped to the grch37 human reference genome using tophat (version 2.0.14) and bowtie2 (version 2.2.9). the read counts and fpkm values […]

PMCID: 5816809

[…] rna-seq using the illumina genome analyzer iix sequencing platform (li et al., 2017b). the raw data of each sample was collected and filtered by the fastx-toolkit ( to get a clean data set that can be further analyzed and processed. the average length of the clean-reads was 100 nt, and the total numbers of clean-reads reached 3,876,126 […]

PMCID: 5861417

[…] at the ncbi-sra under the bioproject accession number prjna378178., quality control and initial cleaning of the reads was performed with the filter by quality program (version 1.0.0) based on fastx-toolkit (blankenberg et al. 2010). reads with less than 90% of bases with phred quality score inferior or equal to 30 were discarded (probability of 1 incorrect base call out of 1,000, […]

PMCID: 5904329

[…] raw data were pretreated from 105 samples and quality control was completed following suyama and matsuki (2015). the programme ‘fastx_trimmer’ in the fastx-toolkit ( was used to trim read 2 sequences including 12 bases of ssr region and two bases of anchor sequences in the 1st primers. the authors used option ‘quality_ filter’ of fastx-toolkit […]

PMCID: 5772623

[…] center for cancer computational biology at dana-farber cancer institute., the bcl files were de-multiplexed using casava v1.82, and the adaptor sequences within the read sequences were trimmed by fastx-toolkit ( the processed sequences were filtered for small rnas greater than 16 nucleotides in length. the sequences were then aligned, quantified […]

FASTX-Toolkit review

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Arup Ghosh

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The tools can calculate quality scores for Fastq files but the statistics are only limited to base calling the quality score. Also, fastx-toolkit has several modules for filtering out low-quality reads.