Oases

Application data
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.

Links

• Oases Mailing list [ edit link ]
• Oases Homepage [ edit link ]
• Oases Source code [ edit link ]

• Add a Link

References

1. . 2012. Bioinformatics (Oxford)

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