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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.

Required Modules


  • gapfiller

System Variables

  • HPC_{{#uppercase:gapfiller}}_DIR


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 ]


  • Validated 4/5/2018