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

被引：576

作者：

Kofler, Robert ^{[1
]}

Pandey, Ram Vinay ^{[1
]}

Schloetterer, Christian ^{[1
]}

机构：

[1] Vetmeduni Vienna, Inst Populat Genet, A-1210 Vienna, Austria

来源：

BIOINFORMATICS | 2011年 / 27卷 / 24期

基金：

奥地利科学基金会;

关键词：

CONTINGENCY-TABLES; LINKAGE; TRAITS;

D O I：

10.1093/bioinformatics/btr589

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 (FST, 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.

引用

页码：3435 / 3436

页数：2

共 21 条

[1]

[Anonymous], 2007, PRINCIPLES POPULATIO

[2] A statistical method for the detection of variants from next-generation resequencing of DNA pools [J].

Bansal, Vikas .

BIOINFORMATICS, 2010, 26 (12) :i318-i324

[3] Population genomics:: Whole-genome analysis of polymorphism and divergence in Drosophila simulans [J].

Begun, David J. ;

Holloway, Alisha K. ;

Stevens, Kristian ;

Hillier, LaDeana W. ;

Poh, Yu-Ping ;

Hahn, Matthew W. ;

Nista, Phillip M. ;

Jones, Corbin D. ;

Kern, Andrew D. ;

Dewey, Colin N. ;

Pachter, Lior ;

Myers, Eugene ;

Langley, Charles H. .

PLOS BIOLOGY, 2007, 5 (11) :2534-2559

[4] Genome-wide analysis of a long-term evolution experiment with Drosophila [J].

Burke, Molly K. ;

Dunham, Joseph P. ;

Shahrestani, Parvin ;

Thornton, Kevin R. ;

Rose, Michael R. ;

Long, Anthony D. .

NATURE, 2010, 467 (7315) :587-U111

[5]

DARVASI A, 1994, GENETICS, V138, P1365

[6] Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows [J].

Excoffier, Laurent ;

Lischer, Heidi E. L. .

MOLECULAR ECOLOGY RESOURCES, 2010, 10 (03) :564-567

[7] On the interpretation of x(2) from contingency tables, and the calculation of P [J].

Fisher, RA .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY, 1922, 85 :87-94

[8] The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples [J].

Futschik, Andreas ;

Schloetterer, Christian .

GENETICS, 2010, 186 (01) :207-218

[9]

HILLEL J, 1990, Animal Biotechnology, V1, P201, DOI 10.1080/10495399009525741

[10] Efficient mapping of mendelian traits in dogs through genome-wide association [J].

Karlsson, Elinor K. ;

Baranowska, Izabella ;

Wade, Claire M. ;

Salmon Hillbertz, Nicolette H. C. ;

Zody, Michael C. ;

Anderson, Nathan ;

Biagi, Tara M. ;

Patterson, Nick ;

Pielberg, Gerli Rosengren ;

Kulbokas, Edward J., III ;

Comstock, Kenine E. ;

Keller, Evan T. ;

Mesirov, Jill P. ;

von Euler, Henrik ;

Kampe, Olle ;

Hedhammar, Ake ;

Lander, Eric S. ;

Andersson, Ran ;

Andersson, Leif ;

Lindblad-Toh, Kerstin .

NATURE GENETICS, 2007, 39 (11) :1321-1328

← 1 2 3 →