Sequence assembler for very short reads.

• Version: 1.2.10
• MAXKMERLENGTH: 31
• Added: November 15, 2012
• Updated: May 27, 2014
• Link: https://www.ebi.ac.uk/~zerbino/velvet/

module avail velvet

The following tool may be helpful in estimating memory requirements for your velvet run:

• http://denovoutils.appspot.com/velvetmem

Make sure you substitute in the correct value for "k" based on the MAXKMERLENGTH used in your Velvet build.

• https://wiki.hpcc.msu.edu/display/Bioinfo/Velvet+and+Oases

Notes from the sysadmin during installation:

wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar xf velvet_1.2.10.tgz
cd velvet_1.2.10
scl enable devtoolset-1.1 bash
sed 's/MAXKMERLENGTH=[0-9].*$/MAXKMERLENGTH=64/' Makefile > Makefile.kmer64
make -f Makefile.kmer64
make -f Makefile.kmer64 cleanobj
sudo cp -r . /export/apps/velvet/1.2.10-kmer64