angsd-wrapper: utilities for analysing next-generation sequencing data.

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  • Additional Information
    • Subject Terms:
    • Author-Supplied Keywords:
      domestication
      population genetics
      software
      visualization
      Zea
    • Abstract:
      High-throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design and data analysis. The software package angsd allows users to perform a number of population genetic analyses on high-throughput sequencing data. angsd uses probabilistic approaches which can directly make use of genotype likelihoods; thus, SNP calling is not required for comparative analyses. This takes advantage of all the sequencing data and produces more accurate results for samples with low sequencing depth. Here, we present angsd-wrapper, a set of wrapper scripts that provides a user-friendly interface for running angsd and visualizing results. angsd-wrapper supports multiple types of analyses including estimates of nucleotide sequence diversity neutrality tests, principal component analysis, estimation of admixture proportions for individual samples and calculation of statistics that quantify recent introgression. angsd-wrapper also provides interactive graphing of angsd results to enhance data exploration. We demonstrate the usefulness of angsd-wrapper by analysing resequencing data from populations of wild and domesticated Zea. angsd-wrapper is freely available from . [ABSTRACT FROM AUTHOR]
    • Abstract:
      Copyright of Molecular Ecology Resources is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
    • ISSN:
      1755-098X
    • Accession Number:
      10.1111/1755-0998.12578
    • Accession Number:
      118762702
  • Citations
    • ABNT:
      DURVASULA, A. et al. angsd-wrapper: utilities for analysing next-generation sequencing data. Molecular Ecology Resources, [s. l.], v. 16, n. 6, p. 1449–1454, 2016. DOI 10.1111/1755-0998.12578. Disponível em: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=hch&AN=118762702. Acesso em: 5 dez. 2020.
    • AMA:
      Durvasula A, Hoffman PJ, Kent TV, et al. angsd-wrapper: utilities for analysing next-generation sequencing data. Molecular Ecology Resources. 2016;16(6):1449-1454. doi:10.1111/1755-0998.12578
    • APA:
      Durvasula, A., Hoffman, P. J., Kent, T. V., Liu, C., Kono, T. J. Y., Morrell, P. L., & Ross, I. J. (2016). angsd-wrapper: utilities for analysing next-generation sequencing data. Molecular Ecology Resources, 16(6), 1449–1454. https://doi.org/10.1111/1755-0998.12578
    • Chicago/Turabian: Author-Date:
      Durvasula, Arun, Paul J. Hoffman, Tyler V. Kent, Chaochih Liu, Thomas J. Y. Kono, Peter L. Morrell, and Ibarra, Jeffrey Ross. 2016. “Angsd-Wrapper: Utilities for Analysing next-Generation Sequencing Data.” Molecular Ecology Resources 16 (6): 1449–54. doi:10.1111/1755-0998.12578.
    • Harvard:
      Durvasula, A. et al. (2016) ‘angsd-wrapper: utilities for analysing next-generation sequencing data’, Molecular Ecology Resources, 16(6), pp. 1449–1454. doi: 10.1111/1755-0998.12578.
    • Harvard: Australian:
      Durvasula, A, Hoffman, PJ, Kent, TV, Liu, C, Kono, TJY, Morrell, PL & Ross, IJ 2016, ‘angsd-wrapper: utilities for analysing next-generation sequencing data’, Molecular Ecology Resources, vol. 16, no. 6, pp. 1449–1454, viewed 5 December 2020, .
    • MLA:
      Durvasula, Arun, et al. “Angsd-Wrapper: Utilities for Analysing next-Generation Sequencing Data.” Molecular Ecology Resources, vol. 16, no. 6, Nov. 2016, pp. 1449–1454. EBSCOhost, doi:10.1111/1755-0998.12578.
    • Chicago/Turabian: Humanities:
      Durvasula, Arun, Paul J. Hoffman, Tyler V. Kent, Chaochih Liu, Thomas J. Y. Kono, Peter L. Morrell, and Ibarra, Jeffrey Ross. “Angsd-Wrapper: Utilities for Analysing next-Generation Sequencing Data.” Molecular Ecology Resources 16, no. 6 (November 2016): 1449–54. doi:10.1111/1755-0998.12578.
    • Vancouver/ICMJE:
      Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, et al. angsd-wrapper: utilities for analysing next-generation sequencing data. Molecular Ecology Resources [Internet]. 2016 Nov [cited 2020 Dec 5];16(6):1449–54. Available from: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=hch&AN=118762702