ANGSD: Analysis of Next Generation Sequencing Data

被引：1851

作者：

Korneliussen, Thorfinn Sand ^{[1
]}

Albrechtsen, Anders ^{[2
]}

Nielsen, Rasmus ^{[1
,3
]}

机构：

[1] Nat Hist Museum Denmark, Ctr GeoGenet, Copenhagen, Denmark

[2] Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark

[3] Univ Calif Berkeley, Dept Integrat Biol & Stat, Berkeley, CA 94720 USA

来源：

BMC BIOINFORMATICS | 2014年 / 15卷

基金：

美国国家卫生研究院; 新加坡国家研究基金会;

关键词：

Next-generation sequencing; Bioinformatics; Population genetics; Association studies; SHORT READ ALIGNMENT; GENOME SEQUENCE; NGS DATA; ASSOCIATION; GENOTYPE; ACCURATE; HISTORY; STATISTICS; DISCOVERY; FRAMEWORK;

D O I：

10.1186/s12859-014-0356-4

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：13

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