Difference between revisions of "BESST"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
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[http://bioinformatics.oxfordjournals.org/content/28/17/2215.long Sahlin K, Street N, Lundeberg J, Arvestad L (2012) "Improved gap size estimation for scaffolding algorithms." Bioinformatics 28(17), 2215-2222]
 
[http://bioinformatics.oxfordjournals.org/content/28/17/2215.long Sahlin K, Street N, Lundeberg J, Arvestad L (2012) "Improved gap size estimation for scaffolding algorithms." Bioinformatics 28(17), 2215-2222]
 +
 
[http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-281 Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281]
 
[http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-281 Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281]
 +
 
[https://bioinformatics.oxfordjournals.org/content/early/2016/03/09/bioinformatics.btw064 Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics]
 
[https://bioinformatics.oxfordjournals.org/content/early/2016/03/09/bioinformatics.btw064 Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics]
  

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