# NextDenovo 2.5.2


{{< admonition success "Installed" true >}}
This software should be available with no extra configuration.
{{< /admonition >}}

## nextdenovo-2.5.2

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, try
[NextPolish](https://github.com/Nextomics/NextPolish).

We benchmarked NextDenovo against other assemblers using Oxford Nanopore long
reads from [human](https://nextdenovo.readthedocs.io/en/latest/TEST2.html) and
[Drosophila
melanogaster](https://nextdenovo.readthedocs.io/en/latest/TEST4.html), and
PacBio continuous long reads (CLR) from [Arabidopsis
thaliana](https://nextdenovo.readthedocs.io/en/latest/TEST3.html). 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.

-------------------------------------------------------------------------------

## Location and version

```console
$ which nextDenovo
/local/cluster/bin/nextDenovo
$ nextDenovo --version
nextDenovo 2.5.2
```

## 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
```

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