ART: a next-generation sequencing read simulator - PubMed (original) (raw)

ART: a next-generation sequencing read simulator

Weichun Huang et al. Bioinformatics. 2012.

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.

PubMed Disclaimer

Similar articles

• NanoSim: nanopore sequence read simulator based on statistical characterization.
  Yang C, Chu J, Warren RL, Birol I. Yang C, et al. Gigascience. 2017 Apr 1;6(4):1-6. doi: 10.1093/gigascience/gix010. Gigascience. 2017. PMID: 28327957 Free PMC article.
• SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.
  Pattnaik S, Gupta S, Rao AA, Panda B. Pattnaik S, et al. BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40. BMC Bioinformatics. 2014. PMID: 24495296 Free PMC article.
• De novo assembly of short sequence reads.
  Paszkiewicz K, Studholme DJ. Paszkiewicz K, et al. Brief Bioinform. 2010 Sep;11(5):457-72. doi: 10.1093/bib/bbq020. Epub 2010 Aug 19. Brief Bioinform. 2010. PMID: 20724458 Review.
• ComB: SNP calling and mapping analysis for color and nucleotide space platforms.
  Souaiaia T, Frazier Z, Chen T. Souaiaia T, et al. J Comput Biol. 2011 Jun;18(6):795-807. doi: 10.1089/cmb.2011.0027. Epub 2011 May 12. J Comput Biol. 2011. PMID: 21563978 Free PMC article.
• A comprehensive evaluation of long read error correction methods.
  Zhang H, Jain C, Aluru S. Zhang H, et al. BMC Genomics. 2020 Dec 21;21(Suppl 6):889. doi: 10.1186/s12864-020-07227-0. BMC Genomics. 2020. PMID: 33349243 Free PMC article. Review.

Cited by

• Computel: computation of mean telomere length from whole-genome next-generation sequencing data.
  Nersisyan L, Arakelyan A. Nersisyan L, et al. PLoS One. 2015 Apr 29;10(4):e0125201. doi: 10.1371/journal.pone.0125201. eCollection 2015. PLoS One. 2015. PMID: 25923330 Free PMC article.
• New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics.
  Knyshov A, Gordon ERL, Weirauch C. Knyshov A, et al. PeerJ. 2021 Mar 31;9:e11019. doi: 10.7717/peerj.11019. eCollection 2021. PeerJ. 2021. PMID: 33850647 Free PMC article.
• VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.
  Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, Johnson J, Dougherty B, Barrett JC, Dry JR. Lai Z, et al. Nucleic Acids Res. 2016 Jun 20;44(11):e108. doi: 10.1093/nar/gkw227. Epub 2016 Apr 7. Nucleic Acids Res. 2016. PMID: 27060149 Free PMC article.
• Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach.
  Srivastava R, Zhang Y, Xiong X, Zhang X, Pan X, Dong XC, Liangpunsakul S, Janga SC. Srivastava R, et al. PLoS One. 2016 Jul 28;11(7):e0160228. doi: 10.1371/journal.pone.0160228. eCollection 2016. PLoS One. 2016. PMID: 27466818 Free PMC article.
• The effect of variant interference on de novo assembly for viral deep sequencing.
  Castro CJ, Marine RL, Ramos E, Ng TFF. Castro CJ, et al. BMC Genomics. 2020 Jun 22;21(1):421. doi: 10.1186/s12864-020-06801-w. BMC Genomics. 2020. PMID: 32571214 Free PMC article.

References

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

Publication types

MeSH terms

Grants and funding

• R01 HG004719/HG/NHGRI NIH HHS/United States
• U01 HG006513/HG/NHGRI NIH HHS/United States
• HG003698/HG/NHGRI NIH HHS/United States
• ES101765/ES/NIEHS NIH HHS/United States
• HG004719/HG/NHGRI NIH HHS/United States
• Z01 ES101765/ImNIH/Intramural NIH HHS/United States
• R01 HG003698/HG/NHGRI NIH HHS/United States

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • Ovid Technologies, Inc.
  • PubMed Central
  • Silverchair Information Systems

• Other Literature Sources

  • The Lens - Patent Citations Database