BESST

Description

besst website  

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]).

Required Modules

Serial

• gcc/5.2.0
• besst

System Variables

• HPC_{{#uppercase:besst}}_DIR - installation 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

Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281

Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics