Difference between revisions of "SHARCGS"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:De Novo]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|sharcgs}} | |{{#vardefine:app|sharcgs}} | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DATA - Sample data directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 22:42, 21 August 2022
Description
SHort-read Assembler based on Robust Contig-extension for Genomic Sequencing.
Environment Modules
Run module spider sharcgs to find out what environment modules are available for this application.
System Variables
- HPC_SHARCGS_DIR - installation directory
- HPC_SHARCGS_DATA - Sample data directory
Citation
If you use the programs or Helicobacter Solexa data for a publication please cite:
Dohm JC, Lottaz C, Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 2007 17: 1697-1706.
If you use Beta vulgaris Solexa data for a publication please cite:
Dohm JC, Lottaz C, Borodina T, Himmelbauer H Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008 Jul 26.[Epub ahead of print]