ART: a next-generation sequencing read simulator

doi:10.1093/bioinformatics/btr708

. 2012 Feb 15;28(4):593-4.

doi: 10.1093/bioinformatics/btr708. Epub 2011 Dec 23.

ART: a next-generation sequencing read simulator

Weichun Huang¹, Leping Li, Jason R Myers, Gabor T Marth

Affiliations

PMID: 22199392
PMCID: PMC3278762
DOI: 10.1093/bioinformatics/btr708

ART: a next-generation sequencing read simulator

Weichun Huang et al. Bioinformatics. 2012.

. 2012 Feb 15;28(4):593-4.

doi: 10.1093/bioinformatics/btr708. Epub 2011 Dec 23.

Authors

Weichun Huang¹, Leping Li, Jason R Myers, Gabor T Marth

Affiliation

¹ Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA. weichun.huang@nih.gov

PMID: 22199392
PMCID: PMC3278762
DOI: 10.1093/bioinformatics/btr708

Abstract

ART is a set of simulation tools that generate synthetic next-generation sequencing reads. This functionality is essential for testing and benchmarking tools for next-generation sequencing data analysis including read alignment, de novo assembly and genetic variation discovery. ART generates simulated sequencing reads by emulating the sequencing process with built-in, technology-specific read error models and base quality value profiles parameterized empirically in large sequencing datasets. We currently support all three major commercial next-generation sequencing platforms: Roche's 454, Illumina's Solexa and Applied Biosystems' SOLiD. ART also allows the flexibility to use customized read error model parameters and quality profiles.

Availability: Both source and binary software packages are available at http://www.niehs.nih.gov/research/resources/software/art.

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References

1. Balzer S., et al. Characteristics of 454 pyrosequencing data–enabling realistic simulation with flowsim. Bioinformatics. 2010;26:i420–i425. - PMC - PubMed
1. Bentley D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 2006;16:545–552. - PubMed
1. Durbin R.M., et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–1073. - PMC - PubMed
1. Huang W., et al. Accurate anchoring alignment of divergent sequences. Bioinformatics. 2006;22:29–34. - PubMed
1. Li H., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079. - PMC - PubMed

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[1] Balzer S., et al. Characteristics of 454 pyrosequencing data–enabling realistic simulation with flowsim. Bioinformatics. 2010;26:i420–i425. - PMC - PubMed

[2] Balzer S., et al. Characteristics of 454 pyrosequencing data–enabling realistic simulation with flowsim. Bioinformatics. 2010;26:i420–i425. - PMC - PubMed

[3] Bentley D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 2006;16:545–552. - PubMed

[4] Bentley D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 2006;16:545–552. - PubMed

[5] Durbin R.M., et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–1073. - PMC - PubMed

[6] Durbin R.M., et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–1073. - PMC - PubMed

[7] Huang W., et al. Accurate anchoring alignment of divergent sequences. Bioinformatics. 2006;22:29–34. - PubMed

[8] Huang W., et al. Accurate anchoring alignment of divergent sequences. Bioinformatics. 2006;22:29–34. - PubMed

[9] Li H., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079. - PMC - PubMed

[10] Li H., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079. - PMC - PubMed

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ART: a next-generation sequencing read simulator

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ART: a next-generation sequencing read simulator

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