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Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

MPS-Authors

Schulz,  Marcel H.
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;
Lane Center for Computational Biology, Carnegie Mellon University;
European Bioinformatics Institute, Wellcome Trust Genome Campus, CBS 10 SD, Hinxton;

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Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Schulz, M. H., Zerbino, D. R., Vingron, M., & Birney, E. (2012). Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28(8), 1086-92. doi:bts094 [pii]10.1093/bioinformatics/bts094 [doi].


Cite as: http://hdl.handle.net/11858/00-001M-0000-000E-E86E-B
Abstract
MOTIVATION: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values. RESULTS: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers. AVAILABILITY AND IMPLEMENTATION: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/.