Quake pipeline

Quake specifications

Information


Unique identifier OMICS_01106
Name Quake
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David Kelley <>

Publication for Quake

Quake IN pipelines

 (12)
2016
PMCID: 4848470
PMID: 27120974
DOI: 10.1038/srep24863

[…] from the truseq adapters, an in-house script to remove low quality portions (quality score <20) at the ends of both reads, jellyfish45 to obtain k-mer frequencies in all the libraries, and quake46 to correct sequencing errors. the data processing resulted in seven libraries that were supplied to platanus47 for genome assembly: 250 bp and 500 bp paired-end libraries, 2 kbp, 6kbp, 15k bp […]

2016
PMCID: 4894063
PMID: 26951782
DOI: 10.1093/gbe/evw045

[…] portions (quality scale < 20) at both ends, jellyfish (marcais and kingsford 2011) to obtain k-mer frequencies in all the libraries (supplementary fig. s1, supplementary material online), and quake (kelley et al. 2010) to correct sequencing errors. the data processing resulted in nine libraries that were supplied to platanus (kajitani et al. 2014) for genome assembly: 250 bp and 500 bp […]

2016
PMCID: 4966470
PMID: 27469966
DOI: 10.1128/genomeA.00746-16

[…] glycol (peg)-nacl solution method (kapa biosystems). a total of 3,165,594 paired-end reads were generated on an illumina miseq, at a read length of 300 bp. reads were error corrected with quake version 0.3.5 (16) and quality filtered and trimmed with trimmomatic version 0.32 (17), resulting in 2,546,326 high-quality reads. the initial sequence assembly was performed using soapdenovo2 […]

2016
PMCID: 5247789
PMID: 28163896
DOI: 10.5256/f1000research.10527.r19231

[…] the truseq adapters, an in-house script to remove low quality portions (quality score < 20) at the ends of both reads, jellyfish 39 v2.2.3 to obtain k-mer frequencies in all the libraries, and quake 40 v0.3.5 to correct sequencing errors. the data processing resulted in seven libraries that were supplied to platanus 41 v1.2.4 for genome assembly: 250 bp and 500 bp paired-end libraries, 2 […]

2015
PMCID: 4393293
PMID: 25860693
DOI: 10.1371/journal.pone.0122928

[…] as well as depth of coverage were determined from the bcl files using custom perl and r scripts., following completion of the sequencing run, sequencing errors in reads were corrected using quake (version 0.3 with a k-mer size of 15) [26], and de novo whole-genome sequence assemblies were generated using spades v. 3.1.1 [27]. detection of a comprehensive set of full length virulence […]

Quake institution(s)
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Quake funding source(s)
Supported by NIH grants R01-LM006845 and R01-GM083873.

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