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lsc website  

LSC is a pure implementation of the long read error correction algorithm. Long reads and high-quality short reads are homopolyer-compressed. Then, compressed short reads are mapped to compressed long reads with either BWA, Bowtie2, RazerS3 or Novoalign. Then the concensus sequences for short reads will replace the mapped regions in the long reads. LSC is geared towards any long reads, as long as they are generated from the same(at least similar) source with the short reads.

Required Modules


  • lsc

We load bowtie, bwa, and novoalign modules for lsc.

System Variables

  • HPC_LSC_DIR - Installation directory.
  • HPC_LSC_CONF - Location of the run.cfg sample run configuration file. Note: copy run.cfg to the working directory and customize it as necessary for the analysis.


  • Validated 4/5/2018