
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.09.04.611267
preprint
1
Article
Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline
Patel Yash http://orcid.org/0000-0003-3113-7010

Zhu Chenghao http://orcid.org/0000-0003-1674-4533

Yamaguchi Takafumi N. http://orcid.org/0000-0003-1082-3871

Wang Nicholas K. http://orcid.org/0000-0003-1043-3072

Wiltsie Nicholas http://orcid.org/0009-0000-7683-5299

Gonzalez Alfredo E. http://orcid.org/0000-0001-8963-3135

Winata Helena K. http://orcid.org/0000-0002-1001-5316

Zeltser Nicole http://orcid.org/0000-0001-7246-2771

Pan Yu
Mootor Mohammed Faizal Eeman http://orcid.org/0000-0003-4154-455X

Sanders Timothy http://orcid.org/0000-0002-5596-323X

Kandoth Cyriac http://orcid.org/0000-0002-1345-3573

Fitz-Gibbon Sorel T. http://orcid.org/0000-0001-7090-5719

Livingstone Julie http://orcid.org/0000-0002-8424-3768

Liu Lydia Y. http://orcid.org/0000-0001-6026-3169

Carlin Benjamin http://orcid.org/0000-0002-9360-9143

Holmes Aaron http://orcid.org/0000-0002-1012-7879

Oh Jieun http://orcid.org/0000-0002-8961-8645

Sahrmann John http://orcid.org/0000-0001-6000-0908

Tao Shu http://orcid.org/0000-0001-5177-6771

Eng Stefan http://orcid.org/0000-0002-5245-6507

Hugh-White Rupert http://orcid.org/0000-0003-3351-8925

Pashminehazar Kiarod http://orcid.org/0009-0007-4824-8733

Park Andrew
Beshlikyan Arpi http://orcid.org/0000-0002-0700-4827

Jordan Madison http://orcid.org/0000-0002-4952-373X

Wu Selina http://orcid.org/0000-0001-5206-0150

Tian Mao http://orcid.org/0000-0002-4418-5153

Arbet Jaron http://orcid.org/0000-0003-4218-2458

Neilsen Beth http://orcid.org/0000-0002-4859-6486

Bugh Yuan Zhe http://orcid.org/0000-0002-3662-3475

Kim Gina http://orcid.org/0000-0001-9265-5490

Salmingo Joseph http://orcid.org/0009-0003-4948-9505

Zhang Wenshu http://orcid.org/0009-0005-1357-3531

Haas Roni http://orcid.org/0000-0003-1505-2965

Anand Aakarsh
Hwang Edward
Neiman-Golden Anna
Steinberg Philippa
Zhao Wenyan http://orcid.org/0000-0001-9647-8006

Anand Prateek
Tsai Brandon L. http://orcid.org/0000-0002-7372-3504

Boutros Paul C. http://orcid.org/0000-0003-0553-7520

07 9 2024
2024.09.04.611267https://creativecommons.org/licenses/by-nc/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.
http://biorxiv.org/lookup/doi/10.1101/2024.09.04.611267
nihpp-2024.09.04.611267.pdf
Abstract

Summary

DNA sequencing is becoming more affordable and faster through advances in high-throughput technologies. This rise in data availability has contributed to the development of novel algorithms to elucidate previously obscure features and led to an increased reliance on complex workflows to integrate such tools into analyses pipelines. To facilitate the analysis of DNA sequencing data, we created metapipeline-DNA, a highly configurable and extensible pipeline. It encompasses a broad range of processing including raw sequencing read alignment and recalibration, variant calling, quality control and subclonal reconstruction. Metapipeline-DNA also contains configuration options to select and tune analyses while being robust to failures. This standardizes and simplifies the ability to analyze large DNA sequencing in both clinical and research settings.

Availability

Metapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is freely available at https://github.com/uclahs-cds/metapipeline-DNA .
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