Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).
Oases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.
Requires the velvet module.
M.H. Schulz, D.R. Zerbino, M. Vingron and Ewan Birney. Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 2012. DOI: 10.1093/bioinformatics/bts094.