Difference between revisions of "BESST"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
 
Line 36: Line 36:
 
-->
 
-->
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 21:13, 6 December 2019

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_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