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ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching

  • Igor MandricEmail author
  • Alex Zelikovsky
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)

Abstract

Next-generation sequencing (NGS) is a powerful technology as it can produce millions of short read pairs covering whole genome; however, a complete genome assembly remains challenging. Usually, assembled genome pieces (i.e., contigs) are merged into chains (i.e., scaffolds) using read pairs mapped to pairs of contigs. A recent comprehensive evaluation of available software shows that the scaffolding problem is still open [1]. In this paper we present a novel scaffolding tool ScaffMatch based on the maximum weight matching of pairs of reverse complement strands representing contigs and further filling the scaffold with skipped short contigs.

Keywords

Read Pair Scaffolding Tool Maximum Weight Match Bundle Size Short Contigs 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Georgia State UniversityAtlantaUSA

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