Difference between revisions of "Oases"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=De novo transcriptome assembler for very short reads | |sw summary=De novo transcriptome assembler for very short reads | ||
| − | |bio domain=RNA-Seq, De-novo assembly, | + | |bio domain=RNA-Seq Alignment, De-novo transcriptome assembly, |
|bio tech=Illumina, ABI SOLiD, 454 | |bio tech=Illumina, ABI SOLiD, 454 | ||
|created by=Schultz MH, Zerbino D | |created by=Schultz MH, Zerbino D | ||
Revision as of 17:04, 13 July 2010
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Application data |
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| Created by | Schultz MH, Zerbino D |
|---|---|
| Biological application domain(s) | RNA-Seq Alignment, De-novo transcriptome assembly |
| Technology | Illumina, ABI SOLiD, 454 |
| Created at | MPI, EBI |
| Maintained? | Yes |
| Programming language(s) | C |
| Licence | GPLv3 |
Summary: De novo transcriptome assembler for very short reads
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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.
Links
References
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