Difference between revisions of "SEQuel"
Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}") |
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| − | [[Category:Software]] | + | [[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 --> | + | |{{#vardefine:exe|1}} <!--RUNNING --> |
|{{#vardefine:conf|}} <!--CONFIGS--> | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | |||
<!--Run--> | <!--Run--> | ||
| + | |||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==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 | ||
|}} | |}} | ||
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 22:39, 21 August 2022
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.
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