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oases-software

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Oases

De novo transcriptome assembler for very short reads.

Information

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.

Usage

Extra info

Installation

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/
oases-software.txt · Last modified: 2014/05/27 13:25 by aorth