Difference between revisions of "BESST"
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==System Variables== | ==System Variables== | ||
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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] | ||
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[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] | ||
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[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 12:51, 15 August 2022
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.
System Variables
- HPC_BESST_DIR - installation directory
Citation
If you publish research that uses besst you have to cite it as follows: