Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an Error
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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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.