Oases

De novo transcriptome assembler for very short reads.

• Version: 0.2.08
• Added: May 27, 2014
• Link: https://www.ebi.ac.uk/~zerbino/oases/

When used in conjunction with one another, Velvet and Oases must be appropriately matched by version/release, and also, based upon the value of MAXKMERLENGTH (the maximum hash length) and CATEGORIES (the number of short read categories), which should also be matched during respective builds.

• Example SLURM scripts: https://github.com/harvardinformatics/bioblog/tree/master/Trinity.Oases.Assembly

Notes from the sysadmin during installation:

wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar zxf velvet_1.2.10.tgz
wget https://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
tar zxf oases_0.2.08.tgz
cd oases_0.2.08
scl enable devtoolset-1.1 bash
make 'VELVET_DIR=../velvet_1.2.10'
sudo mkdir -p /export/apps/oases/0.2.08/bin
sudo cp oases scripts/oases_pipeline.py /export/apps/oases/0.2.08/bin/
sudo cp OasesManual.pdf /export/apps/oases/0.2.08/