Fastq_clean protocols

View Fastq_clean computational protocol

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Fastq_clean specifications


Unique identifier OMICS_26451
Name Fastq_clean
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Some DNA-seq and RNA-seq data from the Illumina sequencer.
Input format FASTQ
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes



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  • person_outline Zhangjun Fei <>
  • person_outline Mi Zhang <>
  • person_outline Honghe Sun <>
  • person_outline Feng Zhan <>
  • person_outline Shan Gao <>

Publication for Fastq_clean

Fastq_clean in pipelines

PMCID: 5405539
PMID: 28446145
DOI: 10.1186/s12864-017-3706-6

[…] by the same method and sequenced on a hiseq 4000 system according to the manufacturer’s instructions with sequenced at 150 bp (pe150, library size is 450–550 bp). the raw reads were filtered with fastq clean software [] to trim low quality (q value < 20) nucleotides on both ends, clipping the adapter and barcode sequences from the 3’ end and discarding the ribosomal rna (rrna) sequence. […]

PMCID: 5485527
PMID: 28621718
DOI: 10.3390/genes8060163

[…] and 3′ rapid amplification of cdna ends (5′ race-pcr and 3′ race-pcr) were used to obtain the complete sequences., the cleaning and quality control of srna-seq data were conducted using the pipeline fastq_clean [] that has been optimized to clean the raw reads from illumina platforms [,,,,,,]. using the software bowtie v.0.12.7 [] with one mismatch, we aligned all the cleaned srna-seq reads […]

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Fastq_clean in publications

PMCID: 5934417
PMID: 29755442
DOI: 10.3389/fmicb.2018.00826

[…] ( the paired-end raw reads from rna-seq were trimmed, thus removing low quality base-calls (q < 30) and adaptor sequences with pipeline fastq_clean (v2.0) (mi et al., ). the cleaned reads were mapped to the reference genome of t. versicolor via star (v2.5.3a) (dobin et al., ; dobin and gingeras, ). the differentially expressed genes […]

PMCID: 5919011
PMID: 29694395
DOI: 10.1371/journal.pone.0195913

[…] steponeplus real-time pcr system. the samples were sequenced on an illumina hiseq 2000 with paired ends (bgi tech, shenzhen, china)., low-quality reads with phred scores < 20 were trimmed using fastq_clean [], and the data quality was assessed using fastqc []. the filtered reads were assembled using trinity (version 2.0.6) with default parameters [, ]. the paired-end reads from each library […]

PMCID: 5595854
PMID: 28900192
DOI: 10.1038/s41598-017-11588-0

[…] steponeplus real-time pcr system. the samples were sequenced with single-end on an illumina hiseqtm 2000 (bgi tech, shenzhen, china)., low-quality reads with phred scores < 20 were trimmed using fastq_clean, and the data quality was assessed using fastqc. the filtered reads were assembled using trinity (version 2.0.6) with default parameters, . the filtered reads from each library […]

PMCID: 5531682
PMID: 28715422
DOI: 10.1371/journal.pntd.0005764

[…] []. adapter sequences were removed using -t (% of occurrence) set to zero. the other parameters were left to their default settings. then deconseq was used to eliminate phix174 phage sequences []. fastq clean files were assembled using spades (version 3.0.0) with the following range of k-mers: 21, 55, 77, 99 and 127 []. we used blastn for sequence comparison between assembled contigs […]

PMCID: 5488377
PMID: 28655295
DOI: 10.1186/s12864-017-3882-4

[…] short read archive (sra) database. the unprocessed rna-seq reads from bioproject erp001341 were then pruned to eliminate low quality base-calls (q < 20) and adaptor sequences using the pipeline fastq clean []. the clean paired reads were mapped to the phyllostachys edulis reference genome using the pipeline tophat2 with the default parameters. briefly, tophat2 uses bowtie2 as an alignment […]

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Fastq_clean institution(s)
School of Computer Science and Technology, Tianjin University, Tianjin, China; Boyce Thompson Institute for Plant Research, Cornell University Ithaca, NY, USA; Department of Computer Science, Guangxi University, Nanning, China; College of Life Science Nankai University, Tianjin, China
Fastq_clean funding source(s)
Supported by the Natural Science Foundation of Jiangxi Province of China (20132BAB214009), the National Natural Science Foundation of China (31201191 and 61170177) and the National Basic Research Program of China (2013CB32930X).

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