Abstract

Abstract Summary: 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 Contact: weichun.huang@nih.gov; gabor.marth@bc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Keywords

Computer scienceBenchmarkingSoftwareData miningSet (abstract data type)Flexibility (engineering)DNA sequencingProcess (computing)Operating systemProgramming languageBiology

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Publication Info

Year
2011
Type
article
Volume
28
Issue
4
Pages
593-594
Citations
1682
Access
Closed

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Weichun Huang, Leping Li, Jason R. Myers et al. (2011). ART: a next-generation sequencing read simulator. Bioinformatics , 28 (4) , 593-594. https://doi.org/10.1093/bioinformatics/btr708

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DOI
10.1093/bioinformatics/btr708