dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods
  • Diploidy
  • Genome / genetics*
  • High-Throughput Nucleotide Sequencing / methods
  • Sequence Analysis, DNA / methods*
  • Software