Oases is a tool for assembling de novo transcriptomes using short RNA-seq reads. The Oases algorithm uses dynamic error removal in the prediction of full-length transcripts, and it can handle a wide range of expression values and the absence of alternative iso-forms. Requires Velvet 1.2.08 or higher (see links).
Transcriptomics; Whole genome sequencing; RNA-Seq; Sequence assembly
Schulz MH, Zerbino DR, Vingron M, Birney E "Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels." Bioinformatics. 2012 Apr 15;28(8):1086-92. Epub 2012 Feb 24. https://doi.org/10.1093/bioinformatics/bts094
PMID: 22368243
PMCID: PMC3324515
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