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NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. It contains two core modules, and use a stepwise fashion to correct the error bases in reference genome. To correct/assemble the raw third-generation sequencing (TGS) long reads with approximately 10-15% sequencing errors, please use NextDenovo.

Environment Modules

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

System Variables

  • HPC_NEXTPOLISH_DIR - installation directory
  • HPC_NEXTPOLISH_BIN - executable directory
  • HPC_NEXTPOLISH_EXE - test data directory