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 <>

Quake article

Quake citations

 (2)
2015
PMCID: 4669482

[…] genome analyzer ii system. raw illumina reads were first processed by removing low-quality reads, adaptor sequences and possible contaminated reads of bacterial and viral origin. then, the software quake36 was used to correct the reads from each library. the corrected reads were then assembled using soapdenovo (-k 63 -r -d), with the three mate-pair libraries being used to link contigs […]

2015
PMCID: 4557055

[…] reads with called bases were stripped of adapters and trimmed using fastx (http://hannonlab.cshl.edu/fastx_toolkit/; appendix s3, supporting information). trimmed reads were error-corrected using quake (kelley et al. 2010) and assembled using soapdenovo v1.05 (li et al. 2010) with a k-mer size of 33 (appendices s4–s5, supporting information). after estimating insert sizes for each library […]

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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