> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/nucleo/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/nucleo/undefined.md).

# 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](/files/-MQnImHOdWGzMPC4aJnF)

## 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>