Alignment of Next-Generation Sequencing Reads

Knut Reinert, Ben Langmead, David Weese, Dirk J. Evers

Research output: Contribution to journalArticle

Abstract

High-throughput DNA sequencing has considerably changed the possibilities for conducting biomedical research by measuring billions of short DNA or RNA fragments. A central computational problem, and for many applications a first step, consists of determining where the fragments came from in the original genome. In this article, we review the main techniques for generating the fragments, the main applications, and the main algorithmic ideas for computing a solution to the read alignment problem. In addition, we describe pitfalls and difficulties connected to determining the correct positions of reads.

Original languageEnglish (US)
Pages (from-to)133-151
Number of pages19
JournalAnnual Review of Genomics and Human Genetics
Volume16
DOIs
StatePublished - Aug 24 2015

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High-Throughput Nucleotide Sequencing
Biomedical Research
Genome
RNA
DNA

Keywords

  • High-throughput sequencing
  • Read mapping
  • String indices

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Molecular Biology

Cite this

Alignment of Next-Generation Sequencing Reads. / Reinert, Knut; Langmead, Ben; Weese, David; Evers, Dirk J.

In: Annual Review of Genomics and Human Genetics, Vol. 16, 24.08.2015, p. 133-151.

Research output: Contribution to journalArticle

Reinert, Knut ; Langmead, Ben ; Weese, David ; Evers, Dirk J. / Alignment of Next-Generation Sequencing Reads. In: Annual Review of Genomics and Human Genetics. 2015 ; Vol. 16. pp. 133-151.
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