https://github.com/steventango/colab-spades
Run SPAdes on Google Colab
https://github.com/steventango/colab-spades
bioinformatics bioinformatics-tool colab-notebook google-colab
Last synced: 4 months ago
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Run SPAdes on Google Colab
- Host: GitHub
- URL: https://github.com/steventango/colab-spades
- Owner: steventango
- License: gpl-2.0
- Created: 2023-09-18T05:21:07.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-10-24T04:21:00.000Z (over 2 years ago)
- Last Synced: 2024-01-28T20:36:19.051Z (over 2 years ago)
- Topics: bioinformatics, bioinformatics-tool, colab-notebook, google-colab
- Language: Jupyter Notebook
- Homepage: https://colab.research.google.com/github/steventango/colab-spades/blob/main/SPAdes_Colab.ipynb
- Size: 18.6 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Colab SPAdes
The Google Colab notebook
[SPAdes_Colab.ipynb](https://colab.research.google.com/github/steventango/colab-spades/blob/main/SPAdes_Colab.ipynb),
can be used to run [SPAdes](https://github.com/ablab/spades) on [Google
Colab](https://colab.research.google.com/).
It uses a precompiled binary of SPAdes that is compatible with Google
Colab.
Using Google Colab for bioinformatics tools like SPAdes is useful as manually installing
tools is not very convenient and web servers hosted by small individual labs are vulnerable
to going down. Google Colab provides free, accessible, and reliable compute and user interface
for bioinformatic tools.
## Compile SPAdes for Colab
We cab use Docker to compile SPAdes for many environments, including Colab.
```bash
docker build --build-arg="SPADES_VERSION=3.15.5" --output . .
gh release create v${SPADES_VERSION} ./SPAdes-${SPADES_VERSION}-Colab.tar.gz
```
## Contributors
- Steven Tang
- Renald Legaspi
## References
```bibtex
@article{Prjibelski2020,
doi = {10.1002/cpbi.102},
url = {https://doi.org/10.1002/cpbi.102},
year = {2020},
month = jun,
publisher = {Wiley},
volume = {70},
number = {1},
author = {Andrey Prjibelski and Dmitry Antipov and Dmitry Meleshko and Alla Lapidus and Anton Korobeynikov},
title = {Using {SPAdes} De Novo Assembler},
journal = {Current Protocols in Bioinformatics}
}
```