Difference between revisions of "MetaVelvet"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:genomics]][[Category:Biology]] |
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|{{#vardefine:app|metavelvet}} | |{{#vardefine:app|metavelvet}} | ||
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Note that MetaVelvet is based on an older version of Velvet than those available on our system. | Note that MetaVelvet is based on an older version of Velvet than those available on our system. | ||
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| − | == | + | ==Environment Modules== |
| − | < | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{uc:{{#var:app}}}}_DIR - | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_{{uc:{{#var:app}}}}_BIN - Executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - Executable directory | ||
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Latest revision as of 19:28, 18 August 2022
Description
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD
MetaVelvet is a single-genome and de Bruijn-graph based assembler Velvet modified and extended for de novo metagenome assembly. The fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome.
Note that MetaVelvet is based on an older version of Velvet than those available on our system.
Environment Modules
Run module spider metavelvet to find out what environment modules are available for this application.
System Variables
- HPC_METAVELVET_DIR - installation directory
- HPC_METAVELVET_BIN - Executable directory