TY - JOUR

T1 - DipSPAdes

T2 - Assembler for Highly Polymorphic Diploid Genomes

AU - Safonova, Yana

AU - Bankevich, Anton

AU - Pevzner, Pavel A.

PY - 2015/6/1

Y1 - 2015/6/1

N2 - 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.

AB - 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.

KW - de Bruijn graphs

KW - diploid genomes

KW - genome assembly

KW - SPAdes assembler

UR - http://www.scopus.com/inward/record.url?scp=84930251984&partnerID=8YFLogxK

U2 - 10.1089/cmb.2014.0153

DO - 10.1089/cmb.2014.0153

M3 - Article

C2 - 25734602

AN - SCOPUS:84930251984

VL - 22

SP - 528

EP - 545

JO - Journal of Computational Biology

JF - Journal of Computational Biology

SN - 1066-5277

IS - 6

ER -