https://github.com/ebedthan/mashphage
Fast and accurate whole-genome clustering of (actino) bacteriophages
https://github.com/ebedthan/mashphage
bioinformatics clustering genome phages
Last synced: 7 months ago
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Fast and accurate whole-genome clustering of (actino) bacteriophages
- Host: GitHub
- URL: https://github.com/ebedthan/mashphage
- Owner: Ebedthan
- License: gpl-3.0
- Created: 2022-02-03T16:21:59.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-02-03T16:43:46.000Z (over 3 years ago)
- Last Synced: 2025-01-22T18:51:25.607Z (9 months ago)
- Topics: bioinformatics, clustering, genome, phages
- Language: Python
- Homepage:
- Size: 13.8 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# mashphage 
[](https://www.gnu.org/licenses/gpl-3.0)
## Fast and accurate whole-genome clustering of (actino) bacteriophages
## Usage
```
mashphage genomes.fa.gz
```
## About
The goal of mashphage is to provide a mean to rapidly and accurately cluster (actino) bacteriophage genome
in know clusters. Mashphage comes bundled with a genomic signature of actinobacteriophage genomes, which enables
to fastly and accurately assign actinobacteriophages genomes in the known cluster schemes.
However, the user can specify a custom path (with `-d` option) to a genomic signature created using `sourmash sketch`.
## Installation
### Last stable release
First install `sourmash`:
```bash
conda install -c conda-forge -c bioconda sourmash
# alternatively you can do
pip install sourmash
```
And install `mashphage` from pypi:
```bash
pip install mashphage
```
### Development version
```bash
# Download ConoDictor development version
git clone https://github.com/Ebedthan/mashphage mashphage
# Navigate to directory
cd mashphage
# Install with poetry: see https://python-poetry.org
poetry install --no-dev
# Enter the Python virtual environment with
poetry shell
# Test mashphage is correctly installed
mashphage -h
```
If you do not want to go into the virtual environment just do:
```bash
poetry run mashphage -h
```
## Bugs
Submit problems or requests to the [Issue Tracker](https://github.com/Ebedthan/mashphage/issues).
## Licence
[GPL v3](https://github.com/Ebedthan/mashphage/blob/main/LICENSE)
## Author
[Anicet Ebou](https://orcid.org/0000-0003-4005-177X)