# PointBlaster
## Installation
pip3 install PointBlaster
## Dependency
- BLAST+ >2.7.0
- cvmblaster (v0.4.0)
**you should add BLAST in your PATH**
## Blast installation
### Windows
Following this tutorial:
[Add blast into your windows PATH](http://82.157.185.121:22300/shares/BevQrP0j8EXn76p7CwfheA)
### Linux/Mac
The easyest way to install blast is:
```
conda install -c bioconda blast
```
## Usage
### 1. Initialize reference database
After finish installation, you should first initialize the reference database using following command
```
PointBlaster -init
```
```
Usage: PointBlaster -i <genome assemble directory> -s <species for point mutation detection> -o <output_directory>
Author: Qingpo Cui(SZQ Lab, China Agricultural University)
optional arguments:
-h, --help show this help message and exit
-i I <input_path>: the PATH to the directory of assembled genome
files. Could not use with -f
-f F <input_file>: the PATH of assembled genome file. Could not
use with -i
-o O <output_directory>: output PATH
-s S <species>: optional var is [salmoenlla, campylobacter],
other species will be supported soon
-minid MINID <minimum threshold of identity>, default=90
-mincov MINCOV <minimum threshold of coverage>, default=60
-list <show species list>
-t T <number of threads>: default=8
-v, --version <display version>
-init <initialize the point mutationdatabase>
```
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