FASTX-Toolkit statistics

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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


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




No version available


  • person_outline FASTX-Toolkit

FASTX-Toolkit citations


DOT1L inhibition attenuates graft versus host disease by allogeneic T cells in adoptive immunotherapy models

Nat Commun
PMCID: 5954061
PMID: 29765028
DOI: 10.1038/s41467-018-04262-0
call_split See protocol

[…] 00 (Illumina) 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 for ea […]


Small RNA profiling of low biomass samples: identification and removal of contaminants

BMC Biol
PMCID: 5952572
PMID: 29759067
DOI: 10.1186/s12915-018-0522-7

[…] hich were subsequently removed using cutadapt []. This step was repeated recursively until no over-represented primer or adapter sequences were detected. 5’-Ns were removed using fastx_clipper of the FASTX-toolkit. Trimmed reads were quality-filtered using fastq_quality_filter of the FASTX-toolkit (with -q 30 -p 90) []. Finally, identical reads were collapsed, retaining the read abundance informat […]


The aquatic animals’ transcriptome resource for comparative functional analysis

BMC Genomics
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] The NGS raw data for the RNA-seq in SRA format were converted to FASTQ format using the SRA-Toolkit v2.2.2 [] and the FASTQ format reads were cleaned to increase read quality by FASTX-Toolkit v0.0.13 ( First, reads with adapters were removed. Second, the sequencing reads were scanned for quality at the reads tails. If the Phred qualit […]


CLIP related methodologies and their application to retrovirology

PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] raw reads into unique reads, demultiplexing samples, discarding short reads (typically less than 15 nucleotides) and trimming the adaptors prior to mapping. One of the most commonly used tools is the FASTX_toolkit (, which provides a number of functions to accomplish all of these steps. Other alternatives, with more limited functions include Cutadapt [], Tr […]


Analysis of LCT 13910 genotypes and bone mineral density in ancient skeletal materials

PLoS One
PMCID: 5927400
PMID: 29708972
DOI: 10.1371/journal.pone.0194966

[…] Sequencing data were processed using a custom analytical pipeline. The script ( was used to separate reads by barcodes using a one mismatch threshold. Cutadapt v1.8.1 software was applied to trim the adap […]


Dicer Like Proteins Regulate Sexual Development via the Biogenesis of Perithecium Specific MicroRNAs in a Plant Pathogenic Fungus Fusarium graminearum

Front Microbiol
PMCID: 5932338
PMID: 29755439
DOI: 10.3389/fmicb.2018.00818

[…] The small RNA analysis and microRNA prediction were performed as previously reported (). After the removal of poor-quality reads and adaptor sequences, clean reads were obtained with the FASTX toolkit. Small sequence reads were completely mapped to the genome of PH-1 from the Ensembl Fungi database using bowtie (). After removal of known non-coding RNAs (rRNA, tRNA, snRNA, and snoRNA) […]


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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.