SEQuel

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_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