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QSRA – a quality-value guided de novo short read assembler

Douglas W Bryant1*, Weng-Keen Wong1 and Todd C Mockler2

Author Affiliations

1 Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, USA

2 Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA

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BMC Bioinformatics 2009, 10:69  doi:10.1186/1471-2105-10-69

Published: 24 February 2009

Abstract

Background

New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data.

Results

We have designed and implemented an assembler, Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality.

Conclusion

QSRA generally produced the highest genomic coverage, while being faster than VCAKE. QSRA is extremely competitive in its longest contig and N50/N80 contig lengths, producing results of similar quality to those of EDENA and VELVET. 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.