# Introduction

![Build Status](https://github.com/msk-access/nucleo/workflows/test_nucleo/badge.svg) [![Updates](https://pyup.io/repos/github/msk-access/nucleo/shield.svg)](https://pyup.io/repos/github/msk-access/nucleo/) [![Python 3](https://pyup.io/repos/github/msk-access/nucleo/python-3-shield.svg)](https://pyup.io/repos/github/msk-access/nucleo/)

* Free software: Apache Software License 2.0
* Documentation: <https://msk-access.gitbook.io/nucleo>

## Features

Given a pair-end fastq file generate collapsed fastq and standard, unfiltered, duplex and simplex Binary Alignment File

![Nucleo](https://1414738465-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LpZ6u2Iz6mdakX0O4CN%2F-MQnHEpYTzwTEPPbyZH9%2F-MQnImHOdWGzMPC4aJnF%2FFgbio-Workflow.png?alt=media\&token=fef4e007-196e-4b46-a8a6-68e6f4b03b4a)

## Installation

Clone the repository:

```
git clone --depth 50 https://github.com/msk-access/nucleo.git
```

## Credits

* CMO cfDNA Informatics Team
* Cookiecutter: <https://github.com/audreyr/cookiecutter>
* `audreyr/cookiecutter-pypackage`: <https://github.com/audreyr/cookiecutter-pypackage>