Difference between revisions of "SEQuel"

Revision as of 21:05, 4 February 2016

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.

Required Modules

modules documentation

Serial

sequel

System Variables

HPC_{{#uppercase:sequel}}_DIR - installation directory

How To Run

Use the 'sequel' script we provide instead of the full 'java -jar...' command.

If needed increase the available memory by setting 'Xmx' in the Java environment variable in your job script or in the shell. E.g.

export _JAVA_OPTIONS="-Xmx6g ${_JAVA_OPTIONS}"

@@ Line 8: / Line 8: @@
 |{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 |{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
-|{{#vardefine:exe|}} <!--RUNNING -->
+|{{#vardefine:exe|1}} <!--RUNNING -->
 |{{#vardefine:conf|}} <!--CONFIGS-->
 |{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
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 {{#if: {{#var: exe}}|==How To Run==
-DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
+Use the 'sequel' script we provide instead of the full 'java -jar...' command.
+If needed increase the available memory by setting 'Xmx' in the Java environment variable in your job script or in the shell. E.g.
+ export _JAVA_OPTIONS="-Xmx6g ${_JAVA_OPTIONS}"
 |}}
 <!--Configuration-->