GapFiller¶
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.
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