General Information
| Description | Robust de novo RNA-seq assembly across the dynamic range of expression levels |
| Homepage | http://www.ebi.ac.uk/~zerbino/oases/ |
Publications
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
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.
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