BESST¶

Description¶

BESST is a package for scaffolding genomic assemblies. It contains several modules for e.g. building a "contig graph" from available information, obtaining scaffolds from this graph, and accurate gap size information (based on GapEst[1]).

Environment Modules¶

Run module spider besst to find out what environment modules are available for this application.

Environment Variables¶

HPC_BESST_DIR - installation directory
HPC_BESST_BIN - executable directory

Citation¶

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

Sahlin, K., Street, N., Lundeberg, J., & Arvestad, L. (2012). Improved gap size estimation for scaffolding algorithms. Bioinformatics, 28(17), 2215–2222. https://doi.org/10.1093/bioinformatics/bts441
Sahlin, K., Vezzi, F., Nystedt, B., Lundeberg, J., & Arvestad, L. (2014). BESST—efficient scaffolding of large fragmented assemblies. BMC Bioinformatics, 15, 281. https://doi.org/10.1186/1471-2105-15-281
Sahlin, K., Chikhi, R., & Arvestad, L. (2016). Assembly scaffolding with PE-contaminated mate-pair libraries. Bioinformatics, 32(13), 1925–1932. https://doi.org/10.1093/bioinformatics/btw064

Categories¶

biology, ngs