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Bioinformatics. 2012 Apr 15;28(8):1086-92. doi: 10.1093/bioinformatics/bts094. Epub 2012 Feb 24.

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

Author information

1
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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/.

PMID:
22368243
PMCID:
PMC3324515
DOI:
10.1093/bioinformatics/bts094
[Indexed for MEDLINE]
Free PMC Article

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