Difference between revisions of "PBJelly"
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− | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Bioinformatics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|PBJelly}} | |{{#vardefine:app|PBJelly}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
− | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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==System Variables== | ==System Variables== | ||
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_CONF |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_TEST |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
− | + | This module includes the full PBSuite. | |
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
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<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
+ | =Validation= | ||
+ | * Validate 4/5/2018 |
Revision as of 21:22, 6 December 2019
Description
PBJelly is a highly automated pipeline that aligns long sequencing reads (such a PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. Each step in PBJelly's workflow can be run on a cluster, thus parallelizing the gap filling process for rapid turn around, even for very large eukaryotic genomes.
Required Modules
Serial
- PBJelly
System Variables
- HPC_PBJELLY_DIR
- HPC_PBJELLY_BIN
- HPC_PBJELLY_CONF
- HPC_PBJELLY_TEST
Additional Information
This module includes the full PBSuite.
Validation
- Validate 4/5/2018