QSRA specifications

Information


Unique identifier OMICS_00026
Name QSRA
Alternative name Quality-value guided Short Read Assembler
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Unassembled reads
Output data Assembled contigs
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 1.0
Stability Stable
Maintained No

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Publication for Quality-value guided Short Read Assembler

QSRA in publications

 (3)
PMCID: 5054208
PMID: 22768980
DOI: 10.1016/j.gpb.2012.05.006

[…] assembly of genomes is marked by three algorithms: short sequence assembly by progressive k-mer search and 3′ read extension (ssake) , verified consensus assembly by k-mer extension (vcake) and quality-value-guided short read assembler (qsra) where each algorithm is an extension of the previous algorithm., ssake proposed for assembly of genomes that were smaller is size (about 30 kb […]

PMCID: 3273484
PMID: 22151917
DOI: 10.1186/1471-2164-12-600

[…] are the following: [genbank:jk523124] to [genbank:jk525007]., we evaluated several assemblers for the de novo assembly of the e. fischeriana root transcriptome, including oases [], velvet [], qsra [], euler-sr [], edena [] and soapdenovo []. preliminary assembled contigs by each tool were blasted against ncbi non-redundant protein database. we found that oases (velvet version 1.0.12 […]

PMCID: 3056720
PMID: 21423806
DOI: 10.1371/journal.pone.0017915

[…] it is also affected by the complexity of dataset. among them, ssake runs in rather less time than other peer assemblers, but the ram usage increases dramatically with augmentation of dataset size. qsra is developed upon the original vcake algorithm, which indeed reduces the computational time, at the cost of ram occupation. sharcgs runs in comparable speed as qsra, however it is highly […]


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QSRA institution(s)
Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
QSRA funding source(s)
Supported by Oregon State University, grant ARF4435 from the Oregon Agricultural Research Foundation, and a NSF Plant Genome Grant DBI 0605240.

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