Difference between revisions of "SEQuel"

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(Created page with " Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|sequel}} |{{#vardefine:url|http://bix.ucsd.edu/SEQuel/index.html}} <!--CONFIGURATION: OPTIONAL (1=ON)...")
 
 
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[[Category:Software]]
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[[Category:Software]][[Category:NGS]][[Category:Biology]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|sequel}}
 
|{{#vardefine:app|sequel}}
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|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 
|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
|{{#vardefine:exe|}} <!--RUNNING -->
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|{{#vardefine:exe|1}} <!--RUNNING -->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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.  
<!--Location-->
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
<!--Versions-->
 
==Available versions==
 
* 1.0.1
 
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Running the application using modules==
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==Environment Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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==System Variables==
 +
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Run-->
 
<!--Run-->
 +
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
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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. set
 +
export _JAVA_OPTIONS="-Xmx6g ${_JAVA_OPTIONS}"
 +
before running something like
 +
sequel -c sample.fasta -ap reads_aln.sam -i 404
 
|}}
 
|}}
 
<!--Configuration-->
 
<!--Configuration-->
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
<!--Policy-->
 
<!--Policy-->
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
|}}
 
|}}

Latest revision as of 22:39, 21 August 2022

Description

sequel website  


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.

Environment Modules

Run module spider sequel to find out what environment modules are available for this application.

System Variables

  • HPC_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. set

export _JAVA_OPTIONS="-Xmx6g ${_JAVA_OPTIONS}"

before running something like

sequel -c sample.fasta -ap reads_aln.sam -i 404