Difference between revisions of "Consed"
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Revision as of 16:30, 10 August 2012
Description
The programs Phrap, Cross_match, and Phred are the leading programs for base calling, sequence comparisons, and sequence assembly. Phred, Cross_match, and Phrap are currently used in many large-scale DNA sequencing and mutation detection projects in academic and biotech settings.
Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.
Execution Environment and Modules
To use consed with the environment modules system at HPC the following commands are available:
Get module information for consed:
$module spider consed
Load the default application module:
$module load consed
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_CONSED_DIR - directory where consed is located.