Introduction

Next-generation sequencing technologies produce short reads that are either de novo assembled or mapped to a reference genome. Genotypes and/or single-nucleotide polymorphisms are then determined from the read composition at each site, which become the basis for many downstream analyses. However, for low sequencing depths, e.g. , there is considerable statistical uncertainty in the assignment of genotypes because of random sampling of homologous base pairs in heterozygotes and sequencing or alignment errors. Recently, several probabilistic methods have been proposed to account for this uncertainty and make accurate inferences from low quality and/or coverage sequencing data. We present ngsTools, a collection of programs to perform population genetics analyses from next-generation sequencing data. The methods implemented in these programs do not rely on single-nucleotide polymorphism or genotype calling and are particularly suitable for low sequencing depth data.Programs included in ngsTools are implemented in C/C++ and are freely available for noncommercial use at https://github.com/mfumagalli/ngsTools.mfumagalli82@gmail.comSupplementary materials are available at Bioinformatics online.

Publications

  1. ngsTools: methods for population genetics analyses from next-generation sequencing data.
    Cite this
    Fumagalli M, Vieira FG, Linderoth T, Nielsen R, 2014-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Matteo Fumagalli
    Developer

    Department of Integrative Biology, Department of Statistics, Denmark

  2. Filipe G Vieira
    Developer

  3. Tyler Linderoth
    Developer

  4. Rasmus Nielsen
    Investigator

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Summary
AccessionBT006522
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByRasmus Nielsen