Introduction

High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously.We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods.The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.

Publications

  1. ANGSD: Analysis of Next Generation Sequencing Data.
    Cite this
    Korneliussen TS, Albrechtsen A, Nielsen R, 2014-11-01 - BMC bioinformatics

Credits

  1. Thorfinn Sand Korneliussen
    Developer

    Centre for GeoGenetics, Natural History Museum of Denmark, Argentina

  2. Anders Albrechtsen
    Developer

    Bioinformatics Centre, Department of Biology, Denmark

  3. Rasmus Nielsen
    Investigator

    Department of Integrative Biology and Statistics, UC-Berkeley

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Summary
AccessionBT005672
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByRasmus Nielsen