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/
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References in zbMATH (referenced in 3 articles )
Showing results 1 to 3 of 3.
- Schulz, Marcel H.; Bar-Joseph, Ziv: Probabilistic models for error correction of nonuniform sequencing data (2017)
- Nimmy, Sonia Farhana; Kamal, M. S.: Next generation sequencing under de novo genome assembly (2015)
- Picardi, Ernesto (ed.): RNA bioinformatics (2015)