Difference between revisions of "Velvet"
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From the [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet web site]: | From the [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet web site]: | ||
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'''Sequence assembler for very short reads.''' | '''Sequence assembler for very short reads.''' | ||
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# All versions were compiled with the Intel Compiler Suite. | # All versions were compiled with the Intel Compiler Suite. | ||
| − | # 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). | + | # 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 [http://www.google.com/url?sa=t&source=web&cd=2&sqi=2&ved=0CBkQFjAB&url=http%3A%2F%2Fhelix.nih.gov%2FApplications%2Fvelvet_manual.pdf&rct=j&q=velvet%20assembler%20manual&ei=Lr1WToqdIsGG0QGJyamyDA&usg=AFQjCNH2VB2-la3kWazMqdl3ms-xkCocVw user manual] for more information). |
# Please file a bugzilla request for additional compile options like color space, different kmers, LONGSEQUENCES, etc. | # Please file a bugzilla request for additional compile options like color space, different kmers, LONGSEQUENCES, etc. | ||
Revision as of 21:24, 25 August 2011
Velvet
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.
Variations
| /apps/velvet/1.1.05/velveth /apps/velvet/1.1.05/velvetg |
Default compilation options (max kmer=31, single threaded) |
| /apps/velvet/1.1.05/velveth_OMP /apps/velvet/1.1.05/velvetg_OMP |
Default kmer, but using OpenMP (see notes below for details) |
| /apps/velvet/1.1.05/velveth_max99_OMP /apps/velvet/1.1.05/velvetg_max99_OMP |
Max kmer of 99 and OpenMP (See notes below for details) |
Notes
- All versions were compiled with the Intel Compiler Suite.
- 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 for additional compile options like 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 # 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