View source for SHARCGS

[[Category:Software]][[Category:biology]][[Category:NGS]][[Category:de novo assembly]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|sharcgs}}
|{{#vardefine:url|http://sharcgs.molgen.mpg.de/index.shtml}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
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<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

SHort-read Assembler based on Robust Contig-extension for Genomic Sequencing.

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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DATA - Sample data directory
<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
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{{#if: {{#var: exe}}|==Additional Information==

WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY

|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==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]

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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