Pittsburgh Supercomputing Center 

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Velvet

Velvet is a de novo sequence assembler for short reads produced by next-generation sequencing technology.

Installed on blacklight.

Other resources that may be helpful include:

 

Running Velvet

To run Velvet you must prepare a batch script and submit it wtih the qsub command. Information about runnng batch jobs on blacklight is available in the "Running Jobs" section of the blacklight user document.

A sample script for running velveth is

#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q batch
##PBS -M <your_email_address>
##PBS -m abe

source /usr/share/modules/init/bash

# load basic velvet with max kmer length of 31
module load velvet/1.2.10

jobid=`echo $PBS_JOBID | cut -f 1 -d '.'`

nthreads=16
export OMP_NUM_THREADS=$nthreads

#move to directory the script was submitted from
cd $PBS_O_WORKDIR

velveth . 19 -short -fasta escherichia_coli_k12.001.fasta escherichia_coli_k12.002.fasta escherichia_coli_k12.003.fasta >& velveth.$jobid.out

 

A sample script for running velvetg is

#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q batch
##PBS -M <your_email_address>
##PBS -m abe

source /usr/share/modules/init/bash

# load basic velvet with max kmer length of 31
module load velvet/1.2.10

jobid=`echo $PBS_JOBID | cut -f 1 -d '.'`

nthreads=16
export OMP_NUM_THREADS=$nthreads

#move to directory the script was submitted from
cd $PBS_O_WORKDIR

velvetg . -cov_cutoff 6 -exp_cov 20 >& velvetg.$jobid.out

 

In your batch script the module load command determines which version of velvet you execute. You can see the available versions of velvet by issuing the command

module avail velvet

If you want to use kmer sizes of 31 or less you must use the module load command

module load velvet/1.2.10

If you want to use kmer sizes of between 32 and 62 you must use the command

module load velvet/1.2.10-maxk62

If you want to use a kmer size greater than 62 you will have to compile your own version.

The data files used by the sample scripts are available for downloading by using the links on the right hand side of this page and in the directory /brashear/projects/examples/velvet on blacklight.