ExSPAnder: a universal repeat resolver for DNA fragment assembly

Bioinformatics. 2014 Jun 15;30(12):i293-301. doi: 10.1093/bioinformatics/btu266.


Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.

Availability and implementation: http://bioinf.spbau.ru/en/spades

Publication types

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

MeSH terms

  • Actinomycetales / genetics
  • Algorithms*
  • DNA / chemistry
  • Gene Library
  • Genome, Bacterial
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Repetitive Sequences, Nucleic Acid
  • Sequence Analysis, DNA / methods*
  • Staphylococcus aureus / genetics


  • DNA