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

• Published in: Bioinformatics (Oxford, England) Vol. 28; no. 8; pp. 1086 - 1092
• Main Authors: Schulz, Marcel H, Zerbino, Daniel R, Vingron, Martin, Birney, Ewan
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.04.2012
• Subjects: Algorithms; Alternative Splicing; Animals; bioinformatics; Biological and medical sciences; computer software; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; General aspects; genetics; genome; high-throughput nucleotide sequencing; High-Throughput Nucleotide Sequencing - methods; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); messenger RNA; methods; Mice; nucleotide sequences; Original Papers; RNA, Messenger; RNA, Messenger - genetics; Sequence Analysis, RNA; Sequence Analysis, RNA - methods; Software; transcriptome; RNA; High throughput sequencing; Dynamics; De novo
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/bts094

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: dzerbino@ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.