Computational methods for discovering structural variation with next-generation sequencing

Nat Methods. 2009 Nov;6(11 Suppl):S13-20. doi: 10.1038/nmeth.1374.


In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions.

Publication types

  • Review

MeSH terms

  • Algorithms
  • Base Sequence
  • Computational Biology / methods*
  • Genetic Variation
  • Genome
  • Genomics / methods*
  • Humans
  • Sequence Analysis, DNA / methods*