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Quality-value guided Short Read Assembler QSRA

Takes advantage of quality-value scores as a further method of dealing with error. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE algorithm by not only drastically reducing runtimes but also increasing the viability of the assembly algorithm through further error handling capabilities. Through the use of quality-values, QSRA can continue contig extension, resulting in longer average contig lengths. QSRA can also output suspected repeated regions to a separate file, aiding in repeat-related analysis.

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QSRA classification

QSRA specifications

Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
Output data:
Assembled contigs
Programming languages:
C++
Version:
1.0
Maintained:
Yes
Interface:
Command line interface
Input data:
Unassembled reads
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable

QSRA distribution

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QSRA support

Maintainer

  • Todd Mockler <>

Credits

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Publications

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

Funding source(s)

This work was supported by Oregon State University, grant ARF4435 from the Oregon Agricultural Research Foundation, and a NSF Plant Genome Grant DBI 0605240.

Link to literature

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