Sequence assembler for very short reads.

• Version: 1.2.10-kmer111
• MAXKMERLENGTH: 111
• Added: November, 2012
• Updated: September, 2017
• 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:

$ cd /tmp
$ wget 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-4 bash
$ sed -i 's/MAXKMERLENGTH=[0-9].*$/MAXKMERLENGTH=111/' Makefile
$ make OPENMP=1
$ make cleanobj
$ sudo cp -r . /export/apps/velvet/1.2.10-kmer111