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Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels.
Bioinformatics. 2012 Feb 24;
Authors: Schulz MH, Zerbino DR, Vingron M, Birney E
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: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.
PMID: 22368243 [PubMed - as supplied by publisher]
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Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels.
Bioinformatics. 2012 Feb 24;
Authors: Schulz MH, Zerbino DR, Vingron M, Birney E
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: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.
PMID: 22368243 [PubMed - as supplied by publisher]
More...