https://github.com/metagentools/metagenomic-database-utilities
Scripts used to create metagenomic databases for metaproteomic analysis
https://github.com/metagentools/metagenomic-database-utilities
Last synced: 12 days ago
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Scripts used to create metagenomic databases for metaproteomic analysis
- Host: GitHub
- URL: https://github.com/metagentools/metagenomic-database-utilities
- Owner: metagentools
- License: bsd-3-clause
- Created: 2022-08-01T03:35:03.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-02-06T04:14:17.000Z (over 2 years ago)
- Last Synced: 2024-02-06T05:26:54.637Z (over 2 years ago)
- Language: Jupyter Notebook
- Size: 19.5 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Metagenomic database utilities
This repository contains scripts used to create metagenomic databases for metaproteomic analysis as part of the analysis for the [ConDiGA](https://github.com/metagentools/ConDiGA) repository.
## File organisation
```
metagenomic-database-utilities
│ environment.yml
│ LICENSE
│ README.md
│
└───scripts
│ │ assemble.sh
│ │ coverm.sh
│ │ kraken2.sh
│ │ metagenemark.sh
│
└───notebooks
│ MD1_UniProt12.ipynb
│ MD2_UniProt12.ipynb
│ MD3_UniProt12.ipynb
```
The scripts use to run other software for assembly, taxonomic classification, gene prediction and coverage calculation are found in the [`scripts`](https://github.com/metagentools/metagenomic-database-utilities/tree/main/scripts) folder.
The steps and code used to create `MD1`, `MD2` and `MD3` databases can be found in the respective notebooks in the [`notebooks`](https://github.com/metagentools/metagenomic-database-utilities/tree/main/notebooks) folder.
## Contacts
Please report any problems in the [issue tracker](https://github.com/metagentools/metagenomic-database-utilities/issues). Also, you can send feedback to [liang_qiao@fudan.edu.cn](mailto:liang_qiao@fudan.edu.cn) or [yu.lin@anu.edu.au](mailto:yu.lin@anu.edu.au).