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NextPolish

(★ 245)

Fast and accurately polish the genome generated by long reads.

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최종 버전 다운로드 (.zip)

- - bug-or-error-report.md
  - question-or-feature-request-.md
- FAQ.rst
- index.rst
- OPTION.rst
- QSTART.rst
- run.cfg
- TEST1.pdf
- TEST1.rst
- TEST2.rst
- TEST3.pdf
- TEST3.rst
- TUTORIAL.rst
- - FAQ.rst
  - index.rst
  - OPTION.rst
  - QSTART.rst
  - run.cfg
  - TEST1.pdf
  - TEST1.rst
  - TEST2.rst
  - TEST3.pdf
  - TEST3.rst
  - TUTORIAL.rst
- - align.c
  - base.c
  - base.h
  - bseq.c
  - bseq.h
  - bsort.c
  - bsort.h
  - calgs.c
  - config.c
  - config.h
  - config_parser.py
  - contig.c
  - contig.h
  - ctg_cns.c
  - ctg_cns.h
  - dag.c
  - kit.py
  - kmercount.c
  - kmercount.h
  - lgspolish.c
  - lgspolish.h
  - main.c
  - Makefile
  - mseq.h
  - nextpolish1.py
  - nextpolish2.py
  - scorechain.c
  - scorechain.h
  - seqlist.c
  - seqlist.h
  - snpphase.c
  - snpphase.h
  - snpvalid.c
  - snpvalid.h
- - genome.nextpolish.fa
  - genome.nextpolishtmp.fa
  - hifi.fasta.gz
  - hifi.fofn
  - hifi.run.cfg
  - lgs.fofn
  - lreads.fasta.gz
  - raw.genome.fasta
  - run.cfg
  - sgs.fofn
  - sreads.R1.fastq.gz
  - sreads.R2.fastq.gz
- - kseq.h
  - Makefile
  - seq_count.c
  - seq_split.c
  - thpool.c
  - thpool.h
- LICENSE
- Makefile
- nextPolish
- README.md
.gitignore
LICENSE
README.md

// repository documentation

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[![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/).