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NextDenovo

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, try NextPolish.

We benchmarked NextDenovo against other assemblers using Oxford Nanopore long reads from human and Drosophila melanogaster, and PacBio continuous long reads (CLR) from Arabidopsis thaliana. NextDenovo produces more contiguous assemblies with fewer contigs compared to the other tools. NextDenovo also shows a high assembly accurate level in terms of assembly consistency and single-base accuracy.

Installation

  • REQUIREMENT

  • INSTALL

    click here or use the following command:

     wget https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz
 tar -vxzf NextDenovo.tgz && cd NextDenovo

    If you want to compile from the source, run:

     git clone [email protected]:Nextomics/NextDenovo.git
 cd NextDenovo && make

  • TEST
    nextDenovo test_data/run.cfg

Learn

  • Quick Start - no experience required, download and assemble now
  • Tutorial - step by step introduction to assemble the HG002 genome
  • FAQ - frequently asked questions
  • Parameter Reference - a detailed introduction about all the parameters
  • Cite - if you get a good assembly with NextDenovo, please cite it

Star

You can track updates by tab the Star button on the upper-right corner at this page.

More

The complete user documentation is available here.