Oases.
Schulz, Marcel H. 1,2,3,+; Zerbino, Daniel R. 3,4,*,+; Vingron, Martin 1; Birney, Ewan 3
[Article] Bioinformatics. 28(8):1086-1092, April 15, 2012.

(Format: HTML, PDF)

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/

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

(C) Copyright Oxford University Press 2012.