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

  • Python (Support python 2 and 3):
    • Paralleltask

• 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

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More

The complete user documentation is available here.