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oases

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  • Version: 0.2.08

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  • oases

oases


De novo transcriptome assembler for very short reads

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.


https://www.ebi.ac.uk/~zerbino/oases/

a quick guide of Velvelt & Oases

Access mode(s):

Command line on saruman.versailles.inra.fr

Keyword(s):

De novo transcriptome assembler short reads

Update: 09 Apr 2015
Creation date: 10 Mar 2015