ART: a next-generation sequencing read simulator
Weichun Huang, Leping Li, Jason R. Myers, Gabor T. Marth- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
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.