ArticleBioinformatics (Oxford, England)2012
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 772 papers.
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772 citing papers in PubMed.
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- Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling metazoan multicellularity, evolution, and adaptation.The Journal of biological chemistry · 2025Article
- De novo transcriptome assembly of the plant Helianthemum marifolium for the study of adaptive mechanisms.Scientific data · 2025Article
- Potential effect ofFrontiers in microbiology · 2025Article
- The lamprey habenula provides an extreme example for the temporal regulation of asymmetric development.Frontiers in cell and developmental biology · 2025Article
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- Minimum flow decomposition in graphs with cycles using integer linear programming.Journal of global optimization : an international journal dealing with theoretical and computational aspects of seeking global optima and their applications in science, management and engineering · 2025Article
- Deep Sequencing Analysis of Virome Components, Viral Gene Expression and Antiviral RNAi Responses inInternational journal of molecular sciences · 2024Article
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Authors and funding
4 authors.
Funding
Abstract
motivationHigh-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.
resultsWe 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.