Cargando…
SNP Discovery through Next-Generation Sequencing and Its Applications
The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in p...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512287/ https://www.ncbi.nlm.nih.gov/pubmed/23227038 http://dx.doi.org/10.1155/2012/831460 |
_version_ | 1782251698286231552 |
---|---|
author | Kumar, Santosh Banks, Travis W. Cloutier, Sylvie |
author_facet | Kumar, Santosh Banks, Travis W. Cloutier, Sylvie |
author_sort | Kumar, Santosh |
collection | PubMed |
description | The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference. |
format | Online Article Text |
id | pubmed-3512287 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
spelling | pubmed-35122872012-12-07 SNP Discovery through Next-Generation Sequencing and Its Applications Kumar, Santosh Banks, Travis W. Cloutier, Sylvie Int J Plant Genomics Review Article The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference. Hindawi Publishing Corporation 2012 2012-11-22 /pmc/articles/PMC3512287/ /pubmed/23227038 http://dx.doi.org/10.1155/2012/831460 Text en Copyright © 2012 Santosh Kumar et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Article Kumar, Santosh Banks, Travis W. Cloutier, Sylvie SNP Discovery through Next-Generation Sequencing and Its Applications |
title | SNP Discovery through Next-Generation Sequencing and Its Applications |
title_full | SNP Discovery through Next-Generation Sequencing and Its Applications |
title_fullStr | SNP Discovery through Next-Generation Sequencing and Its Applications |
title_full_unstemmed | SNP Discovery through Next-Generation Sequencing and Its Applications |
title_short | SNP Discovery through Next-Generation Sequencing and Its Applications |
title_sort | snp discovery through next-generation sequencing and its applications |
topic | Review Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512287/ https://www.ncbi.nlm.nih.gov/pubmed/23227038 http://dx.doi.org/10.1155/2012/831460 |
work_keys_str_mv | AT kumarsantosh snpdiscoverythroughnextgenerationsequencinganditsapplications AT bankstravisw snpdiscoverythroughnextgenerationsequencinganditsapplications AT cloutiersylvie snpdiscoverythroughnextgenerationsequencinganditsapplications |