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

  • Python (Support python 2 and 3):
    • Paralleltask pip install paralleltask

• 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 git@github.com: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

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More

The complete user documentation is available here.