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Release Documentation Status

NextPolish

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. To further improve the consensus accuracy of genomes assembled using HiFi long-reads, please use NextPolish2.

Installation

  • DOWNLOAD
    click here or use the following command:
    wget https://github.com/Nextomics/NextPolish/releases/download/v1.4.1/NextPolish.tgz

    Note: If you get an error like version 'GLIBC_2.14' not found or liblzma.so.0: cannot open shared object file, Please download this version.

  • REQUIREMENT

  • INSTALL

pip install paralleltask
tar -vxzf NextPolish.tgz && cd NextPolish && make

  • UNINSTALL
    cd NextPolish && make clean

  • TEST
    nextPolish test_data/run.cfg

Learn

  • Quick Start - no experience required, download and try now
  • Tutorial - step by step introduction to polish a genome with different types of data
  • FAQ - frequently asked questions
  • Parameter Reference - a detailed introduction about all the parameters
  • Cite - if you get a high accuracy assembly with NextPolish, 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.