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adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.

Abstract

SUMMARY

While the R software is becoming a standard for the analysis of genetic data, classical population genetics tools are being challenged by the increasing availability of genomic sequences. Dedicated tools are needed for harnessing the large amount of information generated by next-generation sequencing technologies. We introduce new tools implemented in the adegenet 1.3-1 package for handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. Using a bit-level coding scheme for SNP data and parallelized computation, adegenet enables the analysis of large genome-wide SNPs datasets using standard personal computers.

AVAILABILITY

adegenet 1.3-1 is available from CRAN: http://cran.r-project.org/web/packages/adegenet/. Information and support including a dedicated forum of discussion can be found on the adegenet website: http://adegenet.r-forge.r-project.org/. adegenet is released with a manual and four tutorials totalling over 300 pages of documentation, and distributed under the GNU General Public Licence (≥2).

CONTACT

t.jombart@imperial.ac.uk.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

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    Source

    Bioinformatics (Oxford, England) 27:21 2011 Nov 1 pg 3070-1

    MeSH

    Genetics, Population
    Genome
    Genome-Wide Association Study
    Genomics
    Polymorphism, Single Nucleotide
    Software

    Pub Type(s)

    Journal Article
    Research Support, N.I.H., Extramural
    Research Support, Non-U.S. Gov't

    Language

    eng

    PubMed ID

    21926124