https://github.com/nextomics/nextdenovo

Fast and accurate de novo assembler for long reads
https://github.com/nextomics/nextdenovo

assembler genome-assembly long-reads oxford-nanopore pacbio

Last synced: 8 months ago
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Fast and accurate de novo assembler for long reads

• Host: GitHub
• URL: https://github.com/nextomics/nextdenovo
• Owner: Nextomics
• License: gpl-3.0
• Created: 2019-01-09T07:39:29.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-05-10T01:23:12.000Z (about 2 years ago)
• Last Synced: 2025-04-05T22:07:58.371Z (about 1 year ago)
• Topics: assembler, genome-assembly, long-reads, oxford-nanopore, pacbio
• Language: C
• Homepage:
• Size: 13.7 MB
• Stars: 387
• Watchers: 17
• Forks: 53
• Open Issues: 48
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# 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, 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.

## Installation

* **REQUIREMENT**

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

		* [Paralleltask](https://github.com/moold/ParallelTask) `pip install paralleltask`

* **INSTALL**  

	click [here](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz) or use the following command:   

	```sh

	wget https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz

	tar -vxzf NextDenovo.tgz && cd NextDenovo

	```   

	If you want to compile from the source, run:

	```sh

	git clone git@github.com:Nextomics/NextDenovo.git

	cd NextDenovo && make

	```

* **TEST**  

`nextDenovo test_data/run.cfg`

## Learn

* [Quick Start](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#quick-start) - no experience required, download and assemble now

* [Tutorial](https://nextdenovo.readthedocs.io/en/latest/TEST1.html) - step by step introduction to assemble the HG002 genome

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

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

* [Cite](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#cite) - if you get a good assembly with NextDenovo, 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://nextdenovo.readthedocs.io/en/latest/).