title: Sequencing depth and coverage: key considerations in genomic analyses.
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)).
authors.affiliation: 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.
authors.forename: David
authors.initials: D
authors.lastname: Sims
authors.affiliation: 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.
authors.forename: Ian
authors.initials: I
authors.lastname: Sudbery
authors.affiliation: 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.
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Ilott
authors.affiliation: 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.
authors.forename: Andreas
authors.initials: A
authors.lastname: Heger
authors.affiliation: 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.
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods*; D017408:Guidelines as Topic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans