Fastaq protocols

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Fastaq specifications

Information


Unique identifier OMICS_19987
Name Fastaq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ, GFF3, EMBL, GBK, Phylip
Output format GZIP
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.15.0
Stability Stable
Source code URL https://codeload.github.com/sanger-pathogens/Fastaq/tar.gz/v3.15.0
Maintained Yes

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Fastaq in pipelines

 (9)
2017
PMCID: 5240211
PMID: 28095784
DOI: 10.1186/s12866-016-0923-0

[…] race core set (takara bio) were used to complement virus sequences of the 5′ end and 3′ end, respectively., all nucleotide sequences determined by miseq (referred to as “reads”) were converted to fastaq format on miseq reporter v2.3 and subsequently analyzed using clc genomics workbench 6.0 (clc bio, cambridge, ma, usa). briefly, the ends of all reads were trimmed to remove adaptor sequences […]

2017
PMCID: 5467800
PMID: 28604782
DOI: 10.1371/journal.pbio.2001855

[…] base as defined by the international union of pure and applied chemistry (iupac) notation was called when the most frequent base was in less than 60% of reads. the programs trimmomatic [] and fastaq [] were used to trim adapters, pcr primers, and low-quality bases from the reads; blastn [] was used to identify contigs and reads suspected of being contaminants; mafft [] was used to align […]

2016
PMCID: 4735820
PMID: 26785770
DOI: 10.1038/ncomms10373

[…] to the miseq illumina (500 cycles) cartridge for a final concentration of 20 pm dna. the sequencing was performed on miseq using paired ends sequencing and default chemistry., we demultiplexed the fastaq file generated by the miseq illumina workflow using casava 1.8.1 (illumina, san diego, usa). we trimmed the sequences for a phred quality score superior to 30 (q>30) using trimmomatic (ref. […]

2016
PMCID: 4909688
PMID: 27376014
DOI: 10.1186/s40064-016-2360-9

[…] provided reagents for cluster amplification and sequencing on the miseq system., real-time image analysis and base calling were performed using the compatible sequencing software rta (illumina). fastaq files were generated using casava (illumina) and loaded onto velvet 1.2.07 for sequence assembly performed on a nf supercomputing server (inspur, shandong, china) (zerbino and birney )., genes […]

2016
PMCID: 4936718
PMID: 27388760
DOI: 10.1371/journal.pone.0158784

[…] hiseq 2500 platform at the beijing genomics institute (bgi americas, san diego, ca)., the basic approach used for transcript assembly and detection of lncrnas is represented in . raw reads in the fastaq files were processed to remove adaptors, low-quality tags and contaminants. to remove the remaining rrna reads, clean reads were mapped to the ribosomal rna (rrna) reference using soft read […]


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Fastaq in publications

 (41)
PMCID: 5896167
PMID: 29590607
DOI: 10.1016/j.celrep.2018.02.103

[…] sequencing on a nano flowcell (2 × 250 base paired-end) with an illumina miseq. image analysis, base calling, de-multiplexing, and data quality assessments were performed on the miseq instrument. fastaq files generated by the miseq were analyzed by pairing and merging the reads using geneious 9.0.5 and subsequently extracting newly acquired spacers by identifying the 3′ end of the degenerate […]

PMCID: 5811047
PMID: 29390040
DOI: 10.1371/journal.ppat.1006858

[…] promoted tolerogenic responses. we further show that the removal of a single bacterial virulence factor, the cnfy toxin, can trigger this process and drives the bacteria into persistency., all fastaq files, files containing gene counts determined by htseq-count of all libraries and lists of identified differentially expressed genes from the different comparisons are available […]

PMCID: 5821459
PMID: 29309035
DOI: 10.7554/eLife.30094.037

[…] created by combining the human genome and orfeus-hs from pld401 (); : orfeus-hs_pld401.gbk). to map sequencing reads onto the reference genome and produce differential gene expression analysis: (1) fastaq files were trimmed via trimmomatic () using the following parameters: -phred33 -threads 8, leading:3 trailing:3 slidingwindow:4:16 minlen:25; (2) mapping was performed via star () version […]

PMCID: 5711903
PMID: 29196717
DOI: 10.1038/s41598-017-17132-4

[…] filters of 88.5% (11,114,000 clusters). within this run, the index representations for all the samples were determined between 0.28 and 3.05% with an average of 1.1%. raw data were configured in fastaq files for r1 and r2 reads between 31 085 to 339 287 paired end reads with an average of 123 741 paired end reads., the bioinformatics analyses were run with minor modifications as described […]

PMCID: 5708779
PMID: 29190814
DOI: 10.1371/journal.pone.0188920

[…] alleles in aromatic rice varieties., data from this study was submitted to ncbi under bioproject id prjna324355 and biosample id samn05200854. raw reads of this project were deposited in compressed fastaq format at sra database of ncbi with the accession number srp076132 (http://www.ncbi.nlm.nih.gov/sra/srp076132)., rice is a major staple food feeding hundreds of millions of people in asia []. […]


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