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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: about 1 month 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 (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2024-05-10T01:23:12.000Z (6 months ago)
- Last Synced: 2024-10-12T20:41:31.968Z (about 1 month ago)
- Topics: assembler, genome-assembly, long-reads, oxford-nanopore, pacbio
- Language: C
- Homepage:
- Size: 13.7 MB
- Stars: 363
- Watchers: 13
- Forks: 53
- Open Issues: 46
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz)
[](https://github.com/Nextomics/NextDenovo/releases)
[](https://nextdenovo.readthedocs.io/en/latest/?badge=latest)
[](https://doi.org/10.1186/s13059-024-03252-4)
# 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 [email protected]: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/).