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.
module spider gapfiller to find out what environment modules are available for this application.
- HPC_GAPFILLER_DIR - installation directory
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 ]