Velvet

Description

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.

In addition to Velvet, as of Velvet version 1.2.06, MetaVelvet-1.1.01 is installed and made available using the same module. There are two versions compiled, meta-velvetg (using a max kmer of 31) and meta-velvetg_MAX99 (using a max kmer of 99).

Other contributed scripts distributed with the Velvet source code (such as VelvetOptimizer) are available in the contrib/ directory: e.g. $HPC_VELVET_DIR/contrib/VelvetOptimiser-2.2.0/VelvetOptimiser.pl.

Required Modules

modules documentation

Serial

velvet

System Variables

HPC_{{#uppercase:velvet}}_DIR - installation directory
HPC_VELVET_BIN - same as above.

Additional Information

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