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

TLDR

High‑throughput sequencing has made the analysis of new model organisms affordable, yet assembling a new genome remains costly, so RNA‑seq is used to sequence mRNA and requires de novo assembly that accounts for alternative isoforms and a wide expression range. The authors introduce Oases, a software package that heuristically assembles RNA‑seq reads without a reference genome across a broad expression spectrum and alternative isoforms. Oases achieves this by employing multiple hash lengths, dynamically filtering noise, robustly resolving alternative splicing events, and efficiently merging several 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. Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/ (contact [e-mail]); supplementary data are available online.

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: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.