ANGSD: Analysis of Next Generation Sequencing Data

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• 作者：Thorfinn Sand Korneliussen (1)
  Anders Albrechtsen (2)
  Rasmus Nielsen (1) (3)
  
  1. Centre for GeoGenetics ; Natural History Museum of Denmark ; Copenhagen ; Denmark
  2. Bioinformatics Centre ; Department of Biology ; University of Copenhagen ; Ole Maaloes Vej 5 ; Copenhagen ; DK-2200 ; Denmark
  3. Department of Integrative Biology and Statistics ; UC-Berkeley ; 4098 VLSB ; Berkeley ; California ; 94720 ; USA
  
• 关键词：Next ; generation sequencing ; Bioinformatics ; Population genetics ; Association studies
• 刊名：BMC Bioinformatics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,220 KB
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• 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
• 出版者：BioMed Central
• ISSN：1471-2105

文摘

Background 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. Results 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. Conclusions 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.