Difference between revisions of "SEQuel"
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SEQuel is a tool for correcting errors (i.e., insertions, deletions, and substitutions) in contigs output from assembly. While assemblies of next generation sequencing (NGS) data are accurate, they still contain a substantial number of errors that need to be corrected after the assembly process. The algorithm behind SEQuel makes use of a graph structure called the ''positional de Bruijn graph'', which models k-mers within reads while incorporating their approximate positions into the model. | SEQuel is a tool for correcting errors (i.e., insertions, deletions, and substitutions) in contigs output from assembly. While assemblies of next generation sequencing (NGS) data are accurate, they still contain a substantial number of errors that need to be corrected after the assembly process. The algorithm behind SEQuel makes use of a graph structure called the ''positional de Bruijn graph'', which models k-mers within reads while incorporating their approximate positions into the model. | ||
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Revision as of 02:36, 10 August 2012
Description
SEQuel is a tool for correcting errors (i.e., insertions, deletions, and substitutions) in contigs output from assembly. While assemblies of next generation sequencing (NGS) data are accurate, they still contain a substantial number of errors that need to be corrected after the assembly process. The algorithm behind SEQuel makes use of a graph structure called the positional de Bruijn graph, which models k-mers within reads while incorporating their approximate positions into the model.
Execution Environment and Modules
To use sequel with the environment modules system at HPC the following commands are available:
Get module information for sequel:
$module spider sequel
Load the default application module:
$module load sequel
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_SEQUEL_DIR - directory where sequel is located.