Sequence assembler for very short reads.
After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrshx or qrsh command.
To add the velvet binaries to the system PATH, execute the following command
module load apps/gcc/4.4.7/velvet/1.2.10
This makes two programs available:-
velvetg - de Bruijn graph construction, error removal and repeat resolution
velveth - simple hashing program
If the command you want to run is velvetg /fastdata/foo1bar/velvet/assembly_31 -exp_cov auto -cov_cutoff auto, here is an example submission script that requests 60 GB of memory
#!/bin/bash
#$ -l rmem=60G
module load apps/gcc/4.4.7/velvet/1.2.10
velvetg /fastdata/foo1bar/velvet/assembly_31 -exp_cov auto -cov_cutoff auto
Put the above into a text file called submit_velvet.sh and submit it to the queue with the command qsub submit_velvet.sh
Velvet has got multicore capabilities but these have not been compiled in our version. This is because there is evidence that the performance is better running in serial than in parallel. See http://www.ehu.eus/ehusfera/hpc/2012/06/20/benchmarking-genetic-assemblers-abyss-vs-velvet/ for details.
Velvet was compiled with gcc 4.4.7
tar -xvzf ./velvet_1.2.10.tgz
cd velvet_1.2.10
make
mkdir -p /usr/local/packages6/apps/gcc/4.4.7/velvet/1.2.10
mv * /usr/local/packages6/apps/gcc/4.4.7/velvet/1.2.10
The module file is on the system at /usr/local/modulefiles/apps/gcc/4.4.7/velvet/1.2.10
Its contents are
#%Module1.0#####################################################################
##
## velvet 1.2.10 module file
##
## Module file logging
source /usr/local/etc/module_logging.tcl
##
proc ModulesHelp { } {
puts stderr "Makes velvet 1.2.10 available"
}
set VELVET_DIR /usr/local/packages6/apps/gcc/4.4.7/velvet/1.2.10
module-whatis "Makes velevt 1.2.10 available"
prepend-path PATH $VELVET_DIR