Difference between revisions of "BESST"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:Bioinformatics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|besst}} |{{#vardefine:url|https://github.com/ksahlin/BE...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| (One intermediate revision by one other user not shown) | |||
| Line 36: | Line 36: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 71: | Line 71: | ||
[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] | ||
Revision as of 21:13, 6 December 2019
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]).
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: