Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels
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ID: 292308
2012
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Abstract
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/ Contact: dzerbino@ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
| Reference Key |
openalex_W2156841387
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|---|---|
| Authors | Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron, Ewan Birney |
| Journal | BMC Bioinformatics |
| Year | 2012 |
| DOI |
10.1093/bioinformatics/bts094
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| URL | |
| Keywords | Keywords not found |
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