From the Velvet web site:
Sequence assembler for very short reads.
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.
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.
|Default compilation options (max kmer=31, single threaded)|
|Default kmer, but using OpenMP (see notes below for details)|
|Max kmer of 99 and OpenMP (See notes below for details)|
Note that 1.1.05 is also still installed in /apps/velvet/1.1.05/ with the same binaries as above.
Running the application using modules
To use Velvet with the environment modules system at HPC the following commands are available:
Get module information for Velvet:
$module spider velvet
Load the application module:
$module load velvet
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
HPC_VELVET_DIR - directory where velvet is located. HPC_VELVET_BIN - same as above.
- The user manual is available here.
- If you use one of the OpenMP versions of velvet, you must set the enviroment variables OMP_NUM_THREADS and OMP_THREAD_LIMIT to the appropriate value based on the processor request in your submission script. For example if you use #PBS -l nodes=1:ppn=8 in your script, also include export OMP_NUM_THREADS=7; export OMP_THREAD_LIMIT=8 (for a bash script) in the script itself (see sample script below and/or the user manual for more information).
- Please file a bugzilla request if you need an executable with different compile-time options such as color space, different kmers, LONGSEQUENCES, etc.
Sample Submission Script
!/bin/bash #PBS -N velvet #PBS -o velvet.out #PBS -e velvet.err #PBS -M <your e-mail addres> #PBS -m abe #PBS -l walltime=12:00:00 #PBS -l pmem=4gb #PBS -l nodes=1:ppn=8 # # Walltime is in the format HH:MM:SS # # In the above PBS directives, pmem represents the per thread memory request so # with ppn=8 and pmem=4gb you are requesting a total of 8x4 = 32GB of RAM. # module load velvet cd $PBS_O_WORKDIR #Set OMP_THREAD_LIMIT--should be the same as ppn above export OMP_THREAD_LIMIT=8 #Set OMP_NUM_THREADS--should be 1 lower than ppn export OMP_NUM_THREADS=7 velveth_max99_OMP velvet_out/ 45 -fastq.gz -shortPaired my_paired_data.fastq.gz velvetg_max99_OMP velvet_out/ -min_contig_lgth 250 -exp_cov 10 -ins_length 350