PoPoolation2: Identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
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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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Variants were filtered using PoPoolation2 to yield a high-confidence set of 6,534,957 SNVs.
“Variants were finally filtered using PoPoolation2 (80) to yield a high-confidence set of SNVs (n = 6,534,957; filtering steps included a minimum coverage of 8, a minimum variant count of 6, a maximum coverage of 500 for the domestic cat pool, and a maximum coverage of 200 for the wildcat pool).”
From Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication (2014) · cites this paper as [80]
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- Authors
- Kofler, R., Pandey, R. V., & Schlötterer, C.
- Affiliations
- University of Veterinary Medicine Vienna (AT)
- Corresponding author
- Schlötterer, Christian
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-10-23
- Volume
- 27
- Issue
- 24
- Pages
- 3435-3436
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3232374
- OpenAlex
- W2161950199
- Cited by
- 815
- References
- 23
- Citations by year
- 2026: 44 · 2025: 48 · 2024: 68 · 2023: 54 · 2022: 86 · 2021: 83 · 2020: 88 · 2019: 77 · 2018: 64 · 2017: 54 · 2016: 62 · 2015: 34 · 2014: 22 · 2013: 26 · 2012: 2
- FWCI
- 9.98
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Austrian Science Fund (P 22725, P19467)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- pooled DNA sequencing, genetic differentiation, F(ST), Fisher's exact test, Cochran-Mantel-Haenszel test, population genetics software
- MeSH terms
- Animals, Drosophila melanogaster, Genetics, Population, Software, Arabidopsis, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genomics
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