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moold authored May 14, 2019
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[![Issues](https://img.shields.io/github/issues/Nextomics/NextPolish.svg)](https://github.com/Nextomics/NextPolish/issues)

# NextPolish
NextPolish is used to fix base errors (SNP/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 four steps (steps 3 & 4 are optional), and use a stepwise fashion to correct the error bases in reference genome. To correct the raw TGS long reads with approximately 15-10% sequencing errors, please use [NextDenovo](https://github.com/Nextomics/NextDenovo).
NextPolish is used to fix base errors (SNP/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 four steps (steps 3 & 4 are optional), and use a stepwise fashion to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use [NextDenovo](https://github.com/Nextomics/NextDenovo).

* **DOWNLOAD**
click [here](https://github.com/Nextomics/NextPolish/releases/download/v1.0.1/NextPolish.tgz) or use the following command:
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[General] # global options
job_type = sge # [local, sge, pbs...]. (default: sge)
job_prefix = nextPolish # prefix tag for jobs. (default: nextPolish)
task = best # task need to run [all, default, best, 1, 2, 3, 4, 12, 123, 12123...], all=1234, default=12, best=12121212. (default: default)
task = best # task need to run [all, default, best, 1, 2, 3, 4, 12, 123, 12123...], all=1234, default=12, best=12121212. (default: default)
rewrite = no # overwrite existed directory [yes, no]. (default: no)
rerun = 3 # re-run unfinished jobs untill finished or reached ${rerun} loops, 0=no. (default: 3)
parallel_jobs = 30 # number of tasks used to run in parallel. (default: 30)
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