https://github.com/msk-access/nucleo
Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK
https://github.com/msk-access/nucleo
bam msk-access umi
Last synced: 4 months ago
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Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK
- Host: GitHub
- URL: https://github.com/msk-access/nucleo
- Owner: msk-access
- License: other
- Created: 2019-06-18T17:27:11.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2025-03-27T13:53:35.000Z (about 1 year ago)
- Last Synced: 2025-03-27T14:49:30.453Z (about 1 year ago)
- Topics: bam, msk-access, umi
- Language: Common Workflow Language
- Homepage: https://cmo-ci.gitbook.io/nucleo/
- Size: 951 KB
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
---
description: Workflow that creates all the bam files for the MSK-ACCESS fastq file
---
# Nucleo: FASTQ to MSK-ACCESS BAM's Generation
 [](https://pyup.io/repos/github/msk-access/nucleo/) [](https://pyup.io/repos/github/msk-access/nucleo/)
- Free software: Apache Software License 2.0
- Documentation: [https://msk-access.gitbook.io/nucleo](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
## 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](https://github.com/audreyr/cookiecutter)
- `audreyr/cookiecutter-pypackage`: [https://github.com/audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage)