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PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

Summary: Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a r...

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Detalles Bibliográficos
Autores principales: Kofler, Robert, Pandey, Ram Vinay, Schlötterer, Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232374/
https://www.ncbi.nlm.nih.gov/pubmed/22025480
http://dx.doi.org/10.1093/bioinformatics/btr589
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author Kofler, Robert
Pandey, Ram Vinay
Schlötterer, Christian
author_facet Kofler, Robert
Pandey, Ram Vinay
Schlötterer, Christian
author_sort Kofler, Robert
collection PubMed
description Summary: Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a range of commonly used measures of differentiation (F(ST), Fisher's exact test and Cochran-Mantel-Haenszel test) that can be applied on different scales (windows, genes, exons, SNPs). The result may be visualized with the widely used Integrated Genomics Viewer. Availability and Implementation: PoPoolation2 is implemented in Perl and R. It is freely available on http://code.google.com/p/popoolation2/ Contact: christian.schloetterer@vetmeduni.ac.at Supplementary Information: Manual: http://code.google.com/p/popoolation2/wiki/Manual Test data and tutorial: http://code.google.com/p/popoolation2/wiki/Tutorial Validation: http://code.google.com/p/popoolation2/wiki/Validation
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spelling pubmed-32323742011-12-07 PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq) Kofler, Robert Pandey, Ram Vinay Schlötterer, Christian Bioinformatics Applications Note Summary: Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a range of commonly used measures of differentiation (F(ST), Fisher's exact test and Cochran-Mantel-Haenszel test) that can be applied on different scales (windows, genes, exons, SNPs). The result may be visualized with the widely used Integrated Genomics Viewer. Availability and Implementation: PoPoolation2 is implemented in Perl and R. It is freely available on http://code.google.com/p/popoolation2/ Contact: christian.schloetterer@vetmeduni.ac.at Supplementary Information: Manual: http://code.google.com/p/popoolation2/wiki/Manual Test data and tutorial: http://code.google.com/p/popoolation2/wiki/Tutorial Validation: http://code.google.com/p/popoolation2/wiki/Validation Oxford University Press 2011-12-15 2011-10-23 /pmc/articles/PMC3232374/ /pubmed/22025480 http://dx.doi.org/10.1093/bioinformatics/btr589 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Kofler, Robert
Pandey, Ram Vinay
Schlötterer, Christian
PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
title PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
title_full PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
title_fullStr PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
title_full_unstemmed PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
title_short PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
title_sort popoolation2: identifying differentiation between populations using sequencing of pooled dna samples (pool-seq)
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232374/
https://www.ncbi.nlm.nih.gov/pubmed/22025480
http://dx.doi.org/10.1093/bioinformatics/btr589
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