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BMC Bioinformatics. 2014 Nov 25;15:356. doi: 10.1186/s12859-014-0356-4.

ANGSD: Analysis of Next Generation Sequencing Data.

Author information

1
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. thorfinn@binf.ku.dk.
2
Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark. albrecht@binf.ku.dk.
3
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. rasmus_nielsen@berkeley.edu.
4
Department of Integrative Biology and Statistics, UC-Berkeley, 4098 VLSB, Berkeley, California, 94720, USA. rasmus_nielsen@berkeley.edu.

Abstract

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.

PMID:
25420514
PMCID:
PMC4248462
DOI:
10.1186/s12859-014-0356-4
[Indexed for MEDLINE]
Free PMC Article
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