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J Comput Biol. 2015 Jun;22(6):528-45. doi: 10.1089/cmb.2014.0153. Epub 2015 Mar 3.

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.

Author information

1
1Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia.
2
2St. Petersburg State University, St. Petersburg, Russia.
3
3Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California.

Abstract

While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP genomes that significantly improves on the state-of-the-art assemblers for HP diploid genomes.

KEYWORDS:

SPAdes assembler; de Bruijn graphs; diploid genomes; genome assembly

PMID:
25734602
PMCID:
PMC4449708
DOI:
10.1089/cmb.2014.0153
[Indexed for MEDLINE]
Free PMC Article

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