Difference between revisions of "GapFiller"

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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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==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
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===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
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==System Variables==
 
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
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=Validation=
 
* Validated 4/5/2018
 

Revision as of 20:47, 10 June 2022

Description

gapfiller website  

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 ]