Sense from sequence reads: methods for alignment and assembly

Nat Methods. 2009 Nov;6(11 Suppl):S6-S12. doi: 10.1038/nmeth.1376.


The most important first step in understanding next-generation sequencing data is the initial alignment or assembly that determines whether an experiment has succeeded and provides a first glimpse into the results. In parallel with the growth of new sequencing technologies, several algorithms that align or assemble the large data output of today's sequencing machines have been developed. We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms*
  • Base Sequence
  • Sequence Alignment / instrumentation
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / instrumentation
  • Sequence Analysis, DNA / methods*