ExSPAnder: A universal repeat resolver for DNA fragment assembly

Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus, Pavel A. Pevzner

Research output: Contribution to journalArticlepeer-review

85 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)I293-I301
JournalBioinformatics
Volume30
Issue number12
DOIs
StatePublished - Jun 15 2014

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint

Dive into the research topics of 'ExSPAnder: A universal repeat resolver for DNA fragment assembly'. Together they form a unique fingerprint.

Cite this