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tongzhouxu committed Mar 29, 2024
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# Mashpit
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mashpit/README.html)
![unittest](https://github.com/tongzhouxu/mashpit/actions/workflows/python-app.yml/badge.svg)
[![License: GPL v2](https://img.shields.io/badge/License-GPL_v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
[![PyPI release](https://img.shields.io/pypi/v/mashpit)](https://pypi.python.org/pypi/mashpit/)

Create a database of mash signatures and find the most similar genomes to a target sample

## Dependencies

- Python >= 3.8
- NCBI datasets

## Installation
Install NCBI datasets
### Option 1. Install with Conda/Mamba (Recommended)
```
conda create -n mashpit -c conda-forge -c bioconda 'mashpit=0.9.6'
conda activate mashpit
```
### Option 2. Install with pip
#### 1. Dependency: Install NCBI datasets
```
curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets'
chmod +x datasets
export PATH=$PATH:$PWD
```

Install mashpit using pip:
#### 2. Install mashpit using pip:
```
pip install mashpit
```
Or git clone from github:
#### Or git clone from github:
```
git clone https://github.com/tongzhouxu/mashpit.git
cd mashpit
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