https://github.com/animesh/nextdenovo
Fast and accurate de novo assembler for long reads
Science Score: 23.0%
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Low similarity (13.0%) to scientific vocabulary
Last synced: 10 months ago
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Fast and accurate de novo assembler for long reads
Basic Info
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- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
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Fork of Nextomics/NextDenovo
Created about 4 years ago
· Last pushed over 3 years ago
https://github.com/animesh/NextDenovo/blob/master/
[](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://www.biorxiv.org/content/10.1101/2023.03.09.531669v1) # 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/).
Owner
- Name: Ani
- Login: animesh
- Kind: user
- Location: Norway
- Company: Norwegian University of Science and Technology
- Website: https://www.fuzzylife.org
- Twitter: animesh1977
- Repositories: 749
- Profile: https://github.com/animesh
A medical graduate from Delhi University with post-graduation in bioinformatics from Jawaharlal Nehru University, India.