Sequencing depth and coverage: key considerations in genomic analyses.
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....
| Main Authors: | , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
2014
|
| _version_ | 1826261262457110528 |
|---|---|
| author | Sims, D Sudbery, I Ilott, N Heger, A Ponting, C |
| author_facet | Sims, D Sudbery, I Ilott, N Heger, A Ponting, C |
| author_sort | Sims, D |
| collection | OXFORD |
| description | 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)). |
| first_indexed | 2024-03-06T19:18:46Z |
| format | Journal article |
| id | oxford-uuid:195593bb-dff4-4108-89a4-65292221aa96 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T19:18:46Z |
| publishDate | 2014 |
| record_format | dspace |
| spelling | oxford-uuid:195593bb-dff4-4108-89a4-65292221aa962022-03-26T10:48:26ZSequencing depth and coverage: key considerations in genomic analyses.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:195593bb-dff4-4108-89a4-65292221aa96EnglishSymplectic Elements at Oxford2014Sims, DSudbery, IIlott, NHeger, APonting, CSequencing 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)). |
| spellingShingle | Sims, D Sudbery, I Ilott, N Heger, A Ponting, C Sequencing depth and coverage: key considerations in genomic analyses. |
| title | Sequencing depth and coverage: key considerations in genomic analyses. |
| title_full | Sequencing depth and coverage: key considerations in genomic analyses. |
| title_fullStr | Sequencing depth and coverage: key considerations in genomic analyses. |
| title_full_unstemmed | Sequencing depth and coverage: key considerations in genomic analyses. |
| title_short | Sequencing depth and coverage: key considerations in genomic analyses. |
| title_sort | sequencing depth and coverage key considerations in genomic analyses |
| work_keys_str_mv | AT simsd sequencingdepthandcoveragekeyconsiderationsingenomicanalyses AT sudberyi sequencingdepthandcoveragekeyconsiderationsingenomicanalyses AT ilottn sequencingdepthandcoveragekeyconsiderationsingenomicanalyses AT hegera sequencingdepthandcoveragekeyconsiderationsingenomicanalyses AT pontingc sequencingdepthandcoveragekeyconsiderationsingenomicanalyses |