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 OpenMP notes below for details)|
|Max kmer of 99 and OpenMP (See OpenMP notes below for details)|
Note that all versions were compiled with icc. Please file a bugzilla request for additional compile options like color space, different kmers, LONGSEQUENCES, etc.
If you use one of the OpenMP versions of velvet, you must set the enviromental 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).
From the Velvet manual:
OpenMP allows a program to make use of multiple CPU cores on the same machine. You might have to set the environment variables OMP_NUM_THREADS and OMP_THREAD_LIMIT. Velvet will the use up to OMP_NUM_THREADS+ 1 or OMP_THREAD_LIMIT threads.
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 # HH:MM:SS #PBS -l pmem=4gb # 4GB of RAM per thread, or 4X8=32GB in this case #PBS -l nodes=1:ppn=8 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 /apps/velvet/1.1.05/velveth_max99_OMP velvet_out/ 45 -fastq.gz -shortPaired my_paried_data.fastq.gz /apps/velvet/1.1.05/velvetg_max99_OMP velvet_out/ -min_contig_lgth 250 -exp_cov 10 -ins_length 350