Oases

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Description

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. 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.

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.

Availability

Version 0.2.08

Use

module add oases-0.2.08
oases   # eventually: oases_pipeline.py

It also loads velvet-1.2.10.

For details, see Documentation.

Documentation

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

Licence

GPL 3.0

Program manager

meta@cesnet.cz

Homepage

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