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PMID: 24434847 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Sequencing depth and coverage: key considerations in genomic analyses.

Nature reviews. Genetics ·Vol. 15 ·No. 2 ·2014-02-00 ·Pages 121-32

Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP

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)).

MeSH Terms
Animals Chromatin Immunoprecipitation/methods Gene Expression Profiling/methods Genomics/methods Guidelines as Topic High-Throughput Nucleotide Sequencing/methods Humans
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Sims David
Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, Parks Road, Oxford OX1 3PT, UK.
Sudbery Ian
Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, Parks Road, Oxford OX1 3PT, UK.
Ilott Nicholas E
Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, Parks Road, Oxford OX1 3PT, UK.
Heger Andreas
Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, Parks Road, Oxford OX1 3PT, UK.
Ponting Chris P
Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, Parks Road, Oxford OX1 3PT, UK.
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Article Info
Journal
Nature reviews. Genetics
Abbr.
Nat Rev Genet
ISSN
1471-0064
DOI
10.1038/nrg3642
Published
2014-02-00
Pages
121-32
Language
English
Region
England
NLM ID
100962779
Subset
IM
Grants
Medical Research Council · MC_EX_G1000902 · United Kingdom
Medical Research Council · MC_EX_UU_G1000902 · United Kingdom
Medical Research Council · MC_U137761446 · United Kingdom
Medical Research Council · MC_UU_12021/1 · United Kingdom
External Links
PubMed source DOI: 10.1038/nrg3642 View journal details
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