fastq-tools protocols

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fastq-tools specifications

Information


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

Subtools


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

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fastq-tools in pipelines

 (33)
2018
PMCID: 5788982
PMID: 29379047
DOI: 10.1038/s41598-018-19820-1

[…] based on this information the resulting reads were trimmed at both ends. nucleotide positions with a score lower than 20 were also masked (replaced by an n). these analyses were performed using the fastq tools implemented in the galaxy platform,. the total number of reads for each transcriptome is presented in supplementary table . to assess the changing rate of new gene detection as a function […]

2018
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 (http://www.ncbi.nlm.nih.gov/traces/sra). fastq files were then processed as previously described. briefly, data were aligned using bowtie2, […]

2018
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 olego and bedgraph files were generated using bedtools to facilitate visualization of read […]

2018
PMCID: 5865718
PMID: 29570716
DOI: 10.1371/journal.pgen.1007258

[…] of reads studied and recovery rates for 5s and 45s informative reads was summarized in ., all data were downloaded in sra format and converted into fastq files by the ncbi sra toolkit’s command (fastq-dump). fastq files were quality and adapter trimmed with trim galore. the trimming criteria required minimal quality score (> 20) and length (>50 bp). next, we identified hi-c reads […]

2018
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] reference genome hg19 for hct116 cells and mm8 for mouse liver using bowtie2, and filtered according to alignment scores using samtools. sra files were converted to fastq format using the command fastq-dump in the sra toolkit (https://github.com/ncbi/sra-tools) before the alignment. peaks were called using macs2 without the --broad option and filtered with the criterion that the enrichment […]


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fastq-tools in publications

 (94)
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] reference genome hg19 for hct116 cells and mm8 for mouse liver using bowtie2, and filtered according to alignment scores using samtools. sra files were converted to fastq format using the command fastq-dump in the sra toolkit (https://github.com/ncbi/sra-tools) before the alignment. peaks were called using macs2 without the --broad option and filtered with the criterion that the enrichment […]

PMCID: 5938774
PMID: 29664388
DOI: 10.3201/eid2405.171700

[…] center for biotechnology information assembly and sequence read archive (sra) databases ( table) plus the 42 genomes sequenced in our study. we transformed the sra data to fastq using sra toolkit (fastq-dump –split-files –gzip –skip-technical) (https://trace.ncbi.nlm.nih.gov/traces/sra/sra.cgi?view=toolkit_doc). we performed genome assembly with a5-pipeline (). we performed in silico inference […]

PMCID: 5885306
PMID: 29632618
DOI: 10.1186/s13100-018-0118-3

[…] panel included wgs data from the macaque sample used to build the latest m. mulatta assembly [mmul8.0.1] (additional file )., wgs data were accessed from the ncbi-sra database []. the sra-toolkit (fastq-dump utility) [] was used to download paired-end next generation sequencing reads and convert them from .sra files to interleaved fastq files. we then used nesoni […]

PMCID: 5865718
PMID: 29570716
DOI: 10.1371/journal.pgen.1007258

[…] of reads studied and recovery rates for 5s and 45s informative reads was summarized in ., all data were downloaded in sra format and converted into fastq files by the ncbi sra toolkit’s command (fastq-dump). fastq files were quality and adapter trimmed with trim galore. the trimming criteria required minimal quality score (> 20) and length (>50 bp). next, we identified hi-c reads […]

PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] score less than q30 were discarded. ion proton reads were filtered to 110 bp, and reads with a quality score less than q20 were discarded. processed bam files were converted to fastq files using the fastq-dump option from the ncbi sra toolkit (https://github.com/ncbi/sratoolkit), which were then converted to fasta files using the fq2fa option from idba-ud []. reads were randomly subsampled using […]


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