> 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

Workflow that creates all the bam files for the MSK-ACCESS fastq file

![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>