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Old can be new again: HAPPY whole genome sequencing, mapping and assembly

During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such...

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Autores principales: Jiang, Zhihua, Rokhsar, Daniel S., Harland, Richard M.
Formato: Texto
Lenguaje:English
Publicado: Ivyspring International Publisher 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669597/
https://www.ncbi.nlm.nih.gov/pubmed/19381348
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author Jiang, Zhihua
Rokhsar, Daniel S.
Harland, Richard M.
author_facet Jiang, Zhihua
Rokhsar, Daniel S.
Harland, Richard M.
author_sort Jiang, Zhihua
collection PubMed
description During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such as DNA probes and markers for their localizations, thus constructing the maps. On the other hand, genome sequencing often requires a high-resolution map as a skeleton for whole genome assembly. However, both genome mapping and sequencing have never come together in one pipeline. After reviewing mapping and next-generation sequencing methods, we would like to share our thoughts with the genome community on how to combine the HAPPY mapping technique with the new-generation sequencing, thus integrating two systems into one pipeline, called HAPPY pipeline. The pipeline starts with preparation of a HAPPY panel, followed by multiple displacement amplification for producing a relatively large quantity of DNA. Instead of conventional marker genotyping, the amplified panel DNA samples are subject to new-generation sequencing with barcode method, which allows us to determine the presence/absence of a sequence contig as a traditional marker in the HAPPY panel. Statistical analysis will then be performed to infer how close or how far away from each other these contigs are within a genome and order the whole genome sequence assembly as well. We believe that such a universal approach will play an important role in genome sequencing, mapping, and assembly of many species; thus advancing genome science and its applications in biomedicine and agriculture.
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spelling pubmed-26695972009-04-16 Old can be new again: HAPPY whole genome sequencing, mapping and assembly Jiang, Zhihua Rokhsar, Daniel S. Harland, Richard M. Int J Biol Sci Review During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such as DNA probes and markers for their localizations, thus constructing the maps. On the other hand, genome sequencing often requires a high-resolution map as a skeleton for whole genome assembly. However, both genome mapping and sequencing have never come together in one pipeline. After reviewing mapping and next-generation sequencing methods, we would like to share our thoughts with the genome community on how to combine the HAPPY mapping technique with the new-generation sequencing, thus integrating two systems into one pipeline, called HAPPY pipeline. The pipeline starts with preparation of a HAPPY panel, followed by multiple displacement amplification for producing a relatively large quantity of DNA. Instead of conventional marker genotyping, the amplified panel DNA samples are subject to new-generation sequencing with barcode method, which allows us to determine the presence/absence of a sequence contig as a traditional marker in the HAPPY panel. Statistical analysis will then be performed to infer how close or how far away from each other these contigs are within a genome and order the whole genome sequence assembly as well. We believe that such a universal approach will play an important role in genome sequencing, mapping, and assembly of many species; thus advancing genome science and its applications in biomedicine and agriculture. Ivyspring International Publisher 2009-04-15 /pmc/articles/PMC2669597/ /pubmed/19381348 Text en © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited.
spellingShingle Review
Jiang, Zhihua
Rokhsar, Daniel S.
Harland, Richard M.
Old can be new again: HAPPY whole genome sequencing, mapping and assembly
title Old can be new again: HAPPY whole genome sequencing, mapping and assembly
title_full Old can be new again: HAPPY whole genome sequencing, mapping and assembly
title_fullStr Old can be new again: HAPPY whole genome sequencing, mapping and assembly
title_full_unstemmed Old can be new again: HAPPY whole genome sequencing, mapping and assembly
title_short Old can be new again: HAPPY whole genome sequencing, mapping and assembly
title_sort old can be new again: happy whole genome sequencing, mapping and assembly
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669597/
https://www.ncbi.nlm.nih.gov/pubmed/19381348
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