Difference between revisions of "Velvet"
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| − | + | __NOTOC__ | |
| − | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] | |
| − | + | {|<!--CONFIGURATION: REQUIRED--> | |
| + | |{{#vardefine:app|velvet}} | ||
| + | |{{#vardefine:url|http://www.ebi.ac.uk/~zerbino/velvet/}} | ||
| + | <!--CONFIGURATION: OPTIONAL (1=ON)--> | ||
| + | |{{#vardefine:exe|1}} <!--RUNNING --> | ||
| + | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
| + | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
| + | |{{#vardefine:policy|}} <!--POLICY--> | ||
| + | |{{#vardefine:testing|}} <!--TESTING/PROFILING--> | ||
| + | |{{#vardefine:faq|}} <!--FAQ--> | ||
| + | |{{#vardefine:citation|}} <!--CITATION--> | ||
| + | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
| + | |} | ||
| + | <!--BODY--> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | 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 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. | ||
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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. | 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|MetaVelvet-1.1.01]] was 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. | |
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| − | + | However, in the Velvet module version 1.2.07 only the contributed scripts are present. [[MetaVelvet|MetaVelvet-1.2.01]] is now provided by its own "metavelvet" module. | |
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| + | Velvet memory requirements increase dramatically with each kmer length increase, so the default velveth and velvetg binaries only handle kmers up to 31 bp and we provide additional binaries to handle kmers up to 99, and 249 bp. The binaries are named with _maxNN suffixes e.g. velveth_max249. In addition _OMP suffixes are used to identify the binaries built for multi-threaded usage (see below). | ||
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| + | <!--Modules--> | ||
| + | ==Environment Modules== | ||
| + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_VELVET_BIN - executable directory | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
# 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.] | ||
# 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. | + | # Please file a [https://bugzilla.rc.ufl.edu/ bugzilla] request if you need an executable with different compile-time options such as color space, different kmers, LONGSEQUENCES, etc. |
| − | + | }} | |
| − | + | {{#if: {{#var: pbs}}|==PBS Script Examples== | |
| − | + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | |
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Latest revision as of 17:06, 14 December 2022
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 was 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.
Velvet memory requirements increase dramatically with each kmer length increase, so the default velveth and velvetg binaries only handle kmers up to 31 bp and we provide additional binaries to handle kmers up to 99, and 249 bp. The binaries are named with _maxNN suffixes e.g. velveth_max249. In addition _OMP suffixes are used to identify the binaries built for multi-threaded usage (see below).
Environment Modules
Run module spider velvet to find out what environment modules are available for this application.
System Variables
- HPC_VELVET_DIR - installation directory
- HPC_VELVET_BIN - executable directory
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.