Metadata-Version: 2.1
Name: sbat
Version: 0.0.6
Summary: A tool for strand bias analysis of NGS data
Home-page: https://github.com/alex-skyslakova/strand-bias-analysis-tool
Author: Alexandra Skyslakova
Author-email: alexandra.skyslakova@gmail.com
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Operating System :: Unix
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: Bio (==1.3.8)
Requires-Dist: matplotlib (==3.5.2)
Requires-Dist: numpy (==1.22.3)
Requires-Dist: pandas (==1.4.2)
Requires-Dist: python-dateutil (==2.8.2)
Requires-Dist: pytz (==2022.1)
Requires-Dist: setuptools (==45.2.0)

# Strand Bias Analysis Tool

## Overview
SBAT is a Python command-line tool for detection of strand bias. 
Strand bias is a situation when information from one strand of DNA is overrepresented compared to the information from 
the other strand. It is one of the types of bias that occur in next-generation sequencing data. Strand bias might lead 
to incorrect evaluation of results gained from sequencing data, if the bias is high. 
This tool offers a way of validating quality of the data against strand bias. More about strand bias and development 
of this tool can be found  [here](path to bachelor thesis once it is public). 

The tool uses [Jellyfish](https://github.com/gmarcais/Jellyfish) k-mer counting tool for counting k-mers in the NGS data and compares frequencies of k-mers 
and their complements, creating both statistics and visual analysis of the results of strand bias. 


## Installation 
#### First, <b>Jellyfish</b> must be installed. 
On Debian and Ubuntu with `apt`:
```Shell
sudo apt update
sudo apt install jellyfish
```

On MacOS with `brew`:
```Shell
brew install jellyfish
```

On Arch, it is available from [AUR](https://aur.archlinux.org/packages/jellyfish/).

On Windows, the best option is to use WSL. For other OS or installation from source code, see [here](https://github.com/gmarcais/Jellyfish)

#### After Jellyfish is installed, proceed with SBAT itself:
Installation from pip
```Shell
pip install sbat
```

To install from source code, download the code and run following in the root of the source tree:
```Shell
python3 -m pip install --upgrade build
python3 -m build
pip install -e .
```

## Usage
