Sequencing depth and coverage: key considerations in genomic analyses

David Sims, Ian Sudbery, Nicholas E Ilott, Andreas Heger, Chris P Ponting

Research output: Contribution to journalArticlepeer-review

Abstract

Sequencing technologies have placed a wide range of genomic analyses within the capabilities of many laboratories. However, sequencing costs often set limits to the amount of sequences that can be generated and, consequently, the biological outcomes that can be achieved from an experimental design. In this Review, we discuss the issue of sequencing depth in the design of next-generation sequencing experiments. We review current guidelines and precedents on the issue of coverage, as well as their underlying considerations, for four major study designs, which include de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses (for example, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and chromosome conformation capture (3C)).

Original languageEnglish
Pages (from-to)121-32
Number of pages12
JournalNature Reviews Genetics
Volume15
Issue number2
DOIs
Publication statusPublished - 17 Jan 2014

Keywords

  • Animals
  • Chromatin Immunoprecipitation
  • Gene Expression Profiling
  • Genomics
  • Guidelines as Topic
  • High-Throughput Nucleotide Sequencing
  • Humans

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