Difference between revisions of "GapFiller"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGSCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|gapfiller}} |{{#vardefine:url|http://w...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
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|{{#vardefine:app|gapfiller}} | |{{#vardefine:app|gapfiller}} | ||
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. The GapFiller method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. | De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. The GapFiller method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. | ||
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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== | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
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| + | Marten Boetzer and Walter Pirovano. ''Toward almost closed genomes with GapFiller''. Genome Biology 2012, 13:R56. [ [http://genomebiology.com/2012/13/6/R56 web] ] | ||
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<!--Installation--> | <!--Installation--> | ||
Latest revision as of 16:52, 15 August 2022
Description
GapFiller is an automated tool to reliably close gaps within scaffolds using paired reads.
De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. The GapFiller method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced.
Environment Modules
Run module spider gapfiller to find out what environment modules are available for this application.
System Variables
- HPC_GAPFILLER_DIR - installation directory
Citation
If you publish research that uses gapfiller you have to cite it as follows:
Marten Boetzer and Walter Pirovano. Toward almost closed genomes with GapFiller. Genome Biology 2012, 13:R56. [ web ]