Graph accordance of next-generation sequence assemblies

Guohui Yao, Liang Ye, Hongyu Gao, Patrick Minx, Wesley C. Warren, George M. Weinstock

Research output: Contribution to journalArticle

35 Scopus citations

Abstract

Motivation: No individual assembly algorithm addresses all the known limitations of assembling short-length sequences. Overall reduced sequence contig length is the major problem that challenges the usage of these assemblies. We describe an algorithm to take advantages of different assembly algorithms or sequencing platforms to improve the quality of next-generation sequence (NGS) assemblies. Results: The algorithm is implemented as a graph accordance assembly (GAA) program. The algorithm constructs an accordance graph to capture the mapping information between the target and query assemblies. Based on the accordance graph, the contigs or scaffolds of the target assembly can be extended, merged or bridged together. Extra constraints, including gap sizes, mate pairs, scaffold order and orientation, are explored to enforce those accordance operations in the correct context. We applied GAA to various chicken NGS assemblies and the results demonstrate improved contiguity statistics and higher genome and gene coverage.

Original languageEnglish (US)
Article numberbtr588
Pages (from-to)13-16
Number of pages4
JournalBioinformatics
Volume28
Issue number1
DOIs
StatePublished - Jan 2012

ASJC Scopus subject areas

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

Fingerprint Dive into the research topics of 'Graph accordance of next-generation sequence assemblies'. Together they form a unique fingerprint.

Cite this