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Velvet
Overview
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
Version 1.2.08 is available. The pre-compiled binaries which used the following options:
CATEGORIES = 2 MAXKMERLENGTH = 64
are installed.
Restrictions on use
Velvet is open source under the GNU license. It is available to all users.
Set up procedure
To access the executables please load the modulefile:
module load apps/binapps/velvet/1.2.08
Running the application
Please do not run velvet on the login node. qrsh may be suitable for some work. Computationally intensive work should be submitted to the batch system.
Velvet cannot be run on more than 1 core.
Examples
- Create datasets needed by velvetg in the auto_351 folder via the one hour interactive queue:
qrsh -l inter -l short -V -cwd velveth auto_351 31 -fastq unmapped351.fastq
- Output assembled contigs > 250bp as contigs.fa in the auto_351 folder via the one hour interactive queue:
qrsh -l inter -l short -V -cwd velvetg auto_351 -min_contig_lgth 250
- To do both of the above via a batch job create a submission script containing the following:
## SGE options ## Inherit the login node environment #$ -V ## Use the current directory #$ -cwd velveth auto_351 31 -fastq unmapped351.fastq velvetg auto_351 -min_contig_lgth 250
Further info
- The velvet website and manual.
- Running the commands
velvetgandvelvethwith no options give some help information.