Difference between revisions of "Olego"
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Moskalenko (talk | contribs) (Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|olego}} |{{#vardefine:url|http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation}} <!--CONFIG...") |
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
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OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by strategic searches with very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. OLego supports multi-threading to allow for fast processing of large-scale data. | OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by strategic searches with very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. OLego supports multi-threading to allow for fast processing of large-scale data. | ||
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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_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 17:44, 19 August 2022
Description
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by strategic searches with very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. OLego supports multi-threading to allow for fast processing of large-scale data.
Environment Modules
Run module spider olego to find out what environment modules are available for this application.
System Variables
- HPC_OLEGO_DIR - installation directory