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nextdenovo website  

NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, please use NextPolish.

Environment Modules

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

System Variables

  • HPC_NEXTDENOVO_DIR - installation directory
  • HPC_NEXTDENOVO_BIN - executable directory


If you publish research that uses nextdenovo you have to cite it as follows:

We are now preparing the manuscript of NextDenovo, so if you use NextDenovo now, please cite the official website (