FASTX-Toolkit protocols

FASTX-Toolkit specifications

Information


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

Subtools


  • 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

Download


Versioning


Add your version

Maintainer


  • person_outline FASTX-Toolkit <>

FASTX-Toolkit IN pipelines

 (192)
2018
PMCID: 5752202
PMID: 29297465
DOI: 10.7554/eLife.31216.024

[…] primers used to make probe are listed in supplementary file 2., chip-seq data for the duplication strain were converted into fasta format, trimmed to 70 nt, and filtered for 70 nt long reads using fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit). processed data were snp-parsed with hashmatch (filichkin et al., 2010) using the mauriceville-oakridge snpome (fasta file listing […]

2018
PMCID: 5752202
PMID: 29297465
DOI: 10.7554/eLife.31216.024

[…] supplementary file 2., chip-seq data for the duplication strain were converted into fasta format, trimmed to 70 nt, and filtered for 70 nt long reads using fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit). processed data were snp-parsed with hashmatch (filichkin et al., 2010) using the mauriceville-oakridge snpome (fasta file listing both versions of each snp) (pomraning et al., 2011). […]

2018
PMCID: 5766512
PMID: 29330490
DOI: 10.1038/s41598-017-18607-0

[…] generated a total of 20732767, 23210984 and 35385105 reads from three testis libraries of cattleyak, and a total of 55707150, 29469263 and 34228475 reads from three testis libraries of yak., fastx (fastx_toolkit-0.0.13.2) was used to remove the low quality reads and adaptors obtained from the six libraries. the clean reads of these libraries were matched to the latest sanger mirbase […]

2018
PMCID: 5773227
PMID: 29346435
DOI: 10.1371/journal.ppat.1006796

[…] experiments using the recombinant pr8 and sv12 viruses, an optimized analysis pipeline was employed. in this pipeline, the first 4 bases of r2 reads were trimmed using fastx_trimmer from the fastx toolkit (v. 0.0.13; http://hannonlab.cshl.edu/fastx_toolkit/). overlapping paired-end reads were merged into a single read using pandaseq (v. 2.9)[45]. merged reads were processed using […]

2018
PMCID: 5773227
PMID: 29346435
DOI: 10.1371/journal.ppat.1006796

[…] viruses, an optimized analysis pipeline was employed. in this pipeline, the first 4 bases of r2 reads were trimmed using fastx_trimmer from the fastx toolkit (v. 0.0.13; http://hannonlab.cshl.edu/fastx_toolkit/). overlapping paired-end reads were merged into a single read using pandaseq (v. 2.9)[45]. merged reads were processed using filter_fastq_by_primerid_length.pl to identify and extract […]

FASTX-Toolkit review

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Arup Ghosh

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Desktop
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.