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GapFiller

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.

Environment Variables

  • HPC_GAPFILLER_DIR - installation directory
  • HPC_GAPFILLER_BIN - executable directory

Citation

If you publish research that uses gapfiller you have to cite it as follows:

Boetzer, M., & Pirovano, W. (2012). Toward almost closed genomes with GapFiller. Genome Biology, 13(6), R56. https://doi.org/10.1186/gb-2012-13-6-r56

Categories

biology, genomics