Introduction

New applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population.SNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie.nelsoncw@email.sc.edu or austin@biol.sc.eduSupplementary data are available at Bioinformatics online.

Publications

  1. SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.
    Cite this
    Nelson CW, Moncla LH, Hughes AL, 2015-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Chase W Nelson
    Developer

    Department of Biological Sciences, University of South Carolina

  2. Louise H Moncla
    Developer

    Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, United States of America

  3. Austin L Hughes
    Investigator

    Department of Biological Sciences, University of South Carolina

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Summary
AccessionBT001739
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByAustin L Hughes