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 the Velvet module version 1.2.06 MetaVelvet-1.1.01 is made available. There are two versions compiled, meta-velvetg (using a max kmer of 31) and meta-velvetg_MAX99 (using a max kmer of 99). There are also multiple contributed scripts available in the same location as the velvet binaries.

However, in the Velvet module version 1.2.07 only the contributed scripts are present. MetaVelvet-1.2.01 is now provided by its own "metavelvet" module.

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