Oases
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.
License
GPL 3.0
Usage
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