Velvet

Description

From the Velvet web site: Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Version

  • 1.1.05

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Velvet requires the following module file to run:

  • apps/velvet/1.1.05

Running Velvet on CIRCE/SC

The Velvet user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

How to Submit Jobs

Provided is a batch script for running Velvet executables on the cluster. This script can be copied into your work directory (the folder with your input files and database files) so that you can submit batch processes to the queue.

Serial Submit Script

Velveth helps you construct the dataset for the following program, velvetg, and indicate to the system what each sequence file represents.

If, for example, you copied the known test “test_reads.fa” from the known tests directory to $WORK/velvet/data, you would set up a submit script like this:

  • The script below (for testing, name it “velveth-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
#!/bin/bash
#
#SBATCH --comment=velveth-test
#SBATCH --ntasks=1
#SBATCH --job-name=velveth-test
#SBATCH --output=output.%j.velveth-test
#SBATCH --time=01:00:00

#### SLURM 1 processor velveth test to run for 1 hour.

module add apps/velvet/1.1.05
velveth $WORK/velvet/data 21 -shortPaired $WORK/velvet/data/test_reads.fa
  • Note: The k-mer length and categories values have a maximum of 57. See the Velvet Manual for more information about velveth options and syntax.

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./velveth-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Distributed Parallel

  • Velvetg is the core of Velvet where the de Bruijn graph is built then manipulated.

Although velvetg saves some files during the process to avoid useless recalculations, the parameters are not saved from one run to the next.

If, for example, you wish to process the output from your velveth run above (with it’s output stored in $WORK/velvet/data), you would set up a submit script like this:

  • The script below (for testing, name it “velvetg-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
#!/bin/bash
#
#SBATCH --comment=velvetg-test
#SBATCH --ntasks=4
#SBATCH --job-name=velvetg-test
#SBATCH --output=output.%j.velvetg-test
#SBATCH --time=01:00:00

#### SLURM 4 processor velvetg test to run for 1 hour.

module add apps/velvet/1.1.05
mpirun velvetg $WORK/velvet/data -read_trkg yes

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./velvetg-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Please refer to the Additional Documentation section for the Velvet Manual and for more information about velvetg options and syntax.

  • Colorspace versions of the Velvet executables are also available as ‘velveth_de’ and ‘velvetg_de’. Beware that color- and sequence space are incompatible, hence separate sets of executables. In other words, don’t try to hash sequence files with colorspace velvet or vice-versa, under penalty of meaningless results!

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Velvet to the IT Help Desk: rc-help@usf.edu