https://github.com/nextomics/nextpolish

Fast and accurately polish the genome generated by long reads.
https://github.com/nextomics/nextpolish

assembly genome polish

Last synced: 2 days ago
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Fast and accurately polish the genome generated by long reads.

• Host: GitHub
• URL: https://github.com/nextomics/nextpolish
• Owner: Nextomics
• License: gpl-3.0
• Created: 2019-05-08T02:54:34.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2025-01-09T01:21:21.000Z (24 days ago)
• Last Synced: 2025-01-23T21:09:11.482Z (9 days ago)
• Topics: assembly, genome, polish
• Language: C
• Homepage:
• Size: 14.2 MB
• Stars: 217
• Watchers: 6
• Forks: 28
• Open Issues: 44
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
[![Release](https://img.shields.io/github/release/Nextomics/NextPolish.svg)](https://github.com/Nextomics/NextPolish/releases)

[![Documentation Status](https://readthedocs.org/projects/nextpolish/badge/?version=latest)](https://nextpolish.readthedocs.io/en/latest/?badge=latest)

# 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](https://github.com/Nextomics/NextDenovo). To further improve the consensus accuracy of genomes assembled using HiFi long-reads, please use [NextPolish2](https://github.com/Nextomics/NextPolish2).

## Installation

* **DOWNLOAD**  

click [here](https://github.com/Nextomics/NextPolish/releases/latest/download/NextPolish.tgz) 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](https://github.com/Nextomics/NextPolish/releases/latest/download/NextPolish-CentOS6.9.tgz).

* **REQUIREMENT**  

	* [Python](https://www.python.org/download/releases/) (Support python 2 and 3):

		* [Paralleltask](https://github.com/moold/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](https://nextpolish.readthedocs.io/en/latest/QSTART.html#quick-start) - no experience required, download and try now

* [Tutorial](https://nextpolish.readthedocs.io/en/latest/TUTORIAL.html) - step by step introduction to polish a genome with different types of data

* [FAQ](https://nextpolish.readthedocs.io/en/latest/FAQ.html) - frequently asked questions

* [Parameter Reference](https://nextpolish.readthedocs.io/en/latest/OPTION.html) - a detailed introduction about all the parameters

* [Cite](https://nextpolish.readthedocs.io/en/latest/QSTART.html#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](https://nextpolish.readthedocs.io/en/latest/).