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

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].

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E86E-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E86F-9
Genre: Journal Article

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 Creators:
Schulz, Marcel H.1, 2, 3, Author
Zerbino, Daniel R.3, 4, Author
Vingron, Martin5, Author              
Birney, Ewan3, Author
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_persistent22              
2Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA, ou_persistent22              
3European Bioinformatics Institute, Wellcome Trust Genome Campus, CBS 10 SD, Hinxton, Cambridgeshire, UK, ou_persistent22              
4Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA , ou_persistent22              
5Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1479639              

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Free keywords: Algorithms Alternative Splicing Animals Gene Expression Profiling High-Throughput Nucleotide Sequencing/ methods Humans Mice RNA, Messenger/genetics Sequence Analysis, RNA/ methods Software
 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/.

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Language(s): eng - English
 Dates: 2012-02-242012-04
 Publication Status: Published in print
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 Rev. Method: Peer
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 28 (8) Sequence Number: - Start / End Page: 1086 - 92 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991