fastq-tools pipeline

fastq-tools specifications


Unique identifier OMICS_11292
Name fastq-tools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format FASTQ
Operating system Unix/Linux
Computer skills Advanced
Version 0.8
Stability Stable
Maintained Yes


  • fastq-dump
  • fastq-grep
  • fastq-kmers
  • fastq-match
  • fastq-sample
  • fastq-sort
  • fastq-uniq


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fastq-tools IN pipelines

PMCID: 5802526
PMID: 29317610
DOI: 10.1038/s41398-017-0053-y

[…] (chip) experiments performed on two donor samples, for which both neun-positive and neun-negative sorted cell populations were available. sra files were converted to fastq files using fastq-dump, part of the sra toolkit available from ncbi ( fastq files were then processed as previously described12. briefly, data were aligned using […]

PMCID: 5840295
PMID: 29511296
DOI: 10.1038/s41598-018-21371-4

[…] nextgen dna sequencing laboratory of the university of florida interdisciplinary center for biotechnology research. illumina rna-seq reads were de-multiplexed based on sample-specific barcodes using fastq-tools yielding ~30 million reads per sample. reads were mapped to the human genome (hg19) using olego38 and bedgraph files were generated using bedtools to facilitate visualization of read […]

PMCID: 5457141
PMID: 28489004
DOI: 10.7554/eLife.23253.044

[…] and functional analysis of gene lists were performed using the go-elite (zambon et al., 2012)., to examine gene expression in arg in human and mouse neocortex, fastq files were obtained using the fastq-dump program of the sra toolkit from the gene expression omnibus, under the accession numbers gse30765, gse38805, gse65000, and gse66217. these datasets contained 13 human and 21 mouse rna-seq […]

PMCID: 5481429
PMID: 28642491
DOI: 10.1038/s41598-017-04370-9

[…] rna-seq samples from 6 organs, 5 tissues, and 2 cell-types were downloaded from ncbi geo online database (gse16256, specific srr numbers see below) and converted from sra format to fastq using the fastq-dump function of sratoolkit 2.6.3 ( reads were aligned to human reference genome hg19 from ucsc by hisat2 version 2.0.447 using default parameters. […]

PMCID: 5496309
PMID: 28676099
DOI: 10.1186/s13072-017-0140-6

[…] chip-experiments for dsumo, pita, zipic, polycomb, ibf1, cp190 und dctcf [18, 19, 41, 42] were downloaded as sra-archives from ncbi’s short read archive (sra) and converted to fastq format using the fastq-dump tool of the sra toolkit version 2.3.5. reads were processed, and peaks were called as described above. data sets used in this study were:gsm1015404, cp190; gsm1015406, su(hw); gsm1015408, […]

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