# NextDenovo 2.4.0 and NextPolish 1.3.1


## NextDenovo

NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi
and ONT). It uses a "correct-then-assemble" strategy similar to canu (no
correction step for PacBio Hifi reads), but requires significantly less
computing resources and storages. After assembly, the per-base accuracy is about
98-99.8%, to further improve single base accuracy, please use NextPolish.

We benchmarked NextDenovo against other assemblers using Oxford Nanopore long
reads from human and Drosophila melanogaster, and PacBio continuous long reads
(CLR) from Arabidopsis thaliana. NextDenovo produces more contiguous assemblies
with fewer contigs compared to the other tools. NextDenovo also shows a high
assembly accurate level in terms of assembly consistency and single-base
accuracy.

## NextPolish

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.

Location and version:

```console
$ which nextDenovo
/local/cluster/bin/nextDenovo
$ nextDenovo --version
nextDenovo v2.4.0
$ which nextPolish
/local/cluster/bin/nextPolish
$ nextPolish --version
nextPolish v1.3.1
```

help message:

```console
$ nextDenovo --help
usage: nextDenovo [-l FILE] [-v] [-h]

nextDenovo:
	Fast and accurate de novo assembler for long reads
exmples:
	nextDenovo run.cfg

For more information about NextDenovo, see https://github.com/Nextomics/NextDenovo

optional arguments:
  -l FILE, --log FILE  log file (default: pidXXX.log.info)
  -v, --version        show program's version number and exit
  -h, --help           please use the config file to pass parameters

$ nextPolish --help
usage: nextPolish [-l FILE] [-v] [-h]

nextDenovo:
	Fast and accurately polish the genome generated by long reads

exmples:
	nextPolish run.cfg

For more information about NextPolish, see https://github.com/Nextomics/NextPolish

optional arguments:
  -l FILE, --log FILE  log file (default: pidXXX.log.info)
  -v, --version        show program's version number and exit
  -h, --help           please use the config file to pass parameters
```

You can find an example `run.cfg` at
`/local/cluster/NextDenovo/test_data/run.cfg`. I suggest taking a look at the
extended parameters here: <https://nextdenovo.readthedocs.io/en/latest/OPTION.html>

software ref: <https://github.com/Nextomics>  
research ref: <https://nextdenovo.readthedocs.io/en/latest/QSTART.html#cite>  
research ref: <https://nextpolish.readthedocs.io/en/latest/QSTART.html#cite>