Difference between revisions of "Oases"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary=De novo transcriptome | + | |sw summary=De novo transcriptome assembler for very short reads |
| − | |bio domain=RNA-Seq, De-novo assembly, | + | |bio domain=RNA-Seq, De-novo assembly, |
| + | |bio tech=Illumina, ABI SOLiD, 454 | ||
| + | |created by=Schultz MH, Zerbino D | ||
| + | |created at=MPI, EBI | ||
| + | |maintained=Yes | ||
| + | |language=C, | ||
| + | |licence=GPLv3, | ||
}} | }} | ||
| + | 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. | ||
Revision as of 09:45, 6 May 2010
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Application data |
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| Created by | Schultz MH, Zerbino D |
|---|---|
| Biological application domain(s) | RNA-Seq, De-novo 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.
