Fastaq pipeline

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

 (4)
2018
PMCID: 5852579
PMID: 29439418
DOI: 10.3390/genes9020083

[…] in count data was estimated and tested for differential expression; this was based on a model using the negative binomial distribution between nitrate and ammonium group samples., both raw (fastaq files) and processed data (normalised counts) are available on the gene expression omnibus (geo) database (series entry number: gse108616) [35]., mfold was used to predict the secondary […]

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 [53] and fastaq [54] were used to trim adapters, pcr primers, and low-quality bases from the reads; blastn [55] was used to identify contigs and reads suspected of being contaminants; mafft [56] was used […]

2014
PMCID: 4077829
PMID: 24984015
DOI: 10.1371/journal.pone.0101412

[…] human exome 2.1 m array. paired-end sequences of 91 nucleotides from each end were generated using an illumina hiseq 2000 instrument to an average of 50× coverage. sequences were generated in fastaq format., samples were aligned to the human reference genome version hg19 [10] using the bwa aligner software [11] with default parameters. for each patient, all the samples were pre-processed […]

2013
PMCID: 3534699
PMID: 23301059
DOI: 10.1371/journal.pone.0053310

[…] gatk [16], [17] pipeline software., the chi-square test was used for comparison of the enrichment in nucleotide transitions and mutation rate between the adenoma and the adenocarcinoma., raw data (fastaq sequence) has been uploaded to the short read archive database and the accession number is sra052805., somatic single nucleotide variations of the adenoma and the adenocarcinoma were called […]

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