Difference between revisions of "Velvet"

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{| cellspacing="1" cellpadding="1" border="1" style="width: 954px; height: 138px;"
 
{| cellspacing="1" cellpadding="1" border="1" style="width: 954px; height: 138px;"
 
|-
 
|-
−
| /apps/velvet/1.1.05/velveth<br>/apps/velvet/1.1.05/velvetg  
+
| /apps/velvet/1.2.01/velveth<br>/apps/velvet/1.1.05/velvetg  
 
| Default compilation options (max kmer=31, single threaded)
 
| Default compilation options (max kmer=31, single threaded)
 
|-
 
|-
−
| /apps/velvet/1.1.05/velveth_OMP<br>/apps/velvet/1.1.05/velvetg_OMP
+
| /apps/velvet/1.2.01/velveth_OMP<br>/apps/velvet/1.1.05/velvetg_OMP
 
| Default kmer, but using OpenMP (see notes below for details)
 
| Default kmer, but using OpenMP (see notes below for details)
 
|-
 
|-
−
| /apps/velvet/1.1.05/velveth_max99_OMP<br>/apps/velvet/1.1.05/velvetg_max99_OMP
+
| /apps/velvet/1.2.01/velveth_max99_OMP<br>/apps/velvet/1.1.05/velvetg_max99_OMP
 
| Max kmer of 99 and 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.
 +
  
  
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# The user manual is available [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 here.]
 
# The user manual is available [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 here.]
−
# 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 [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).
 
# 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 [https://bugzilla.hpc.ufl.edu/ bugzilla] request if you need an executable with different compile-time options such as color space, different kmers, LONGSEQUENCES, etc.
 
# Please file a [https://bugzilla.hpc.ufl.edu/ bugzilla] request if you need an executable with different compile-time options such as color space, different kmers, LONGSEQUENCES, etc.
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#
 
#
 
   
 
   
 +
module load velvet
 
cd $PBS_O_WORKDIR
 
cd $PBS_O_WORKDIR
 
   
 
   
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export OMP_NUM_THREADS=7
 
export OMP_NUM_THREADS=7
 
   
 
   
−
/apps/velvet/1.1.05/velveth_max99_OMP velvet_out/ 45 -fastq.gz -shortPaired my_paired_data.fastq.gz
+
velveth_max99_OMP velvet_out/ 45 -fastq.gz -shortPaired my_paired_data.fastq.gz
−
/apps/velvet/1.1.05/velvetg_max99_OMP velvet_out/ -min_contig_lgth 250 -exp_cov 10 -ins_length 350
+
velvetg_max99_OMP velvet_out/ -min_contig_lgth 250 -exp_cov 10 -ins_length 350
 
</pre>
 
</pre>

Revision as of 15:13, 23 December 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/1.2.01/velveth
/apps/velvet/1.1.05/velvetg 		Default compilation options (max kmer=31, single threaded)
/apps/velvet/1.2.01/velveth_OMP
/apps/velvet/1.1.05/velvetg_OMP 		Default kmer, but using OpenMP (see notes below for details)
/apps/velvet/1.2.01/velveth_max99_OMP
/apps/velvet/1.1.05/velvetg_max99_OMP 		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.


Notes

  1. The user manual is available here.
  1. 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).
  2. 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
Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Velvet&oldid=5682"