ANGSD: Analysis of Next Generation Sequencing Data

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2014 Nov 26

PMID 25420514

Citations 1052

Authors

Thorfinn Sand Korneliussen

Anders Albrechtsen

Rasmus Nielsen

Affiliations

Soon will be listed here.

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.

Citing Articles

Using genomic selection to correct pedigree errors in kiwiberry breeding.

Mertten D, McKenzie C, Thomson S, McCallum J, Andersen D, Baldwin S Mol Breed. 2025; 45(3):33.

PMID: 40078838 PMC: 11896956. DOI: 10.1007/s11032-025-01552-6.

Investigation of selection signatures of dairy goats using whole-genome sequencing data.

Peng W, Zhang Y, Gao L, Wang S, Liu M, Sun E BMC Genomics. 2025; 26(1):234.

PMID: 40069586 PMC: 11899394. DOI: 10.1186/s12864-025-11437-9.

Genomic selection in a kiwiberry breeding programme: integrating intra- and inter-specific crossing.

Mertten D, McKenzie C, Baldwin S, Thomson S, Souleyre E, Lenhard M Mol Breed. 2025; 45(3):31.

PMID: 40061125 PMC: 11889281. DOI: 10.1007/s11032-025-01550-8.

Ancient DNA analysis of elite nomadic warrior from Chinge-Tey I funerary commemorative complex in the "Valley of the Kings", Tuva.

Nedoluzhko A, Vergasova E, Sharko F, Agapitova N, Kharitonov D, Sukhanova X BMC Genomics. 2025; 26(1):220.

PMID: 40045199 PMC: 11884045. DOI: 10.1186/s12864-025-11361-y.

Impacts of reproductive systems on grapevine genome and breeding.

Xiao H, Wang Y, Liu W, Shi X, Huang S, Cao S Nat Commun. 2025; 16(1):2031.

PMID: 40032836 PMC: 11876636. DOI: 10.1038/s41467-025-56817-7.

References

Kim S, Lohmueller K, Albrechtsen A, Li Y, Korneliussen T, Tian G . Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics. 2011; 12:231. PMC: 3212839. DOI: 10.1186/1471-2105-12-231. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K . SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009; 25(15):1966-7. DOI: 10.1093/bioinformatics/btp336. View

Yu X, Sun S . Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics. 2013; 14:274. PMC: 3848615. DOI: 10.1186/1471-2105-14-274. View

Nielsen R, Paul J, Albrechtsen A, Song Y . Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 2011; 12(6):443-51. PMC: 3593722. DOI: 10.1038/nrg2986. View

Gravel S, Henn B, Gutenkunst R, Indap A, Marth G, Clark A . Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A. 2011; 108(29):11983-8. PMC: 3142009. DOI: 10.1073/pnas.1019276108. View

Browning B, Yu Z . Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies. Am J Hum Genet. 2009; 85(6):847-61. PMC: 2790566. DOI: 10.1016/j.ajhg.2009.11.004. View

Li H . A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011; 27(21):2987-93. PMC: 3198575. DOI: 10.1093/bioinformatics/btr509. View

10.

Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M . Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 2013; 499(7456):74-8. DOI: 10.1038/nature12323. View

11.

Frazer K, Ballinger D, Cox D, Hinds D, Stuve L, Boudreau A . A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007; 449(7164):851-61. PMC: 2689609. DOI: 10.1038/nature06258. View

12.

Raghavan M, Skoglund P, Graf K, Metspalu M, Albrechtsen A, Moltke I . Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 2013; 505(7481):87-91. PMC: 4105016. DOI: 10.1038/nature12736. View

13.

Ewing G, Hermisson J . MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics. 2010; 26(16):2064-5. PMC: 2916717. DOI: 10.1093/bioinformatics/btq322. View

14.

Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J . SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One. 2012; 7(7):e37558. PMC: 3404070. DOI: 10.1371/journal.pone.0037558. View

15.

Albrechtsen A, Nielsen F, Nielsen R . Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol. 2010; 27(11):2534-47. PMC: 3107607. DOI: 10.1093/molbev/msq148. View

16.

Fumagalli M, Vieira F, Korneliussen T, Linderoth T, Huerta-Sanchez E, Albrechtsen A . Quantifying population genetic differentiation from next-generation sequencing data. Genetics. 2013; 195(3):979-92. PMC: 3813878. DOI: 10.1534/genetics.113.154740. View

17.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

18.

Wang Y, Lu J, Yu J, Gibbs R, Yu F . An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res. 2013; 23(5):833-42. PMC: 3638139. DOI: 10.1101/gr.146084.112. View

19.

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

20.

Rasmussen M, Li Y, Lindgreen S, Pedersen J, Albrechtsen A, Moltke I . Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2010; 463(7282):757-62. PMC: 3951495. DOI: 10.1038/nature08835. View