SEQuel: Difference between revisions
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[[Category:Software]] | [[Category:Software]][[Category:NGS]][[Category:Biology]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
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== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
< | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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