Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline
Author:
Patel YashORCID, Zhu ChenghaoORCID, Yamaguchi Takafumi N.ORCID, Wang Nicholas K.ORCID, Wiltsie NicholasORCID, Gonzalez Alfredo E.ORCID, Winata Helena K.ORCID, Zeltser NicoleORCID, Pan Yu, Mootor Mohammed Faizal EemanORCID, Sanders TimothyORCID, Kandoth CyriacORCID, Fitz-Gibbon Sorel T.ORCID, Livingstone JulieORCID, Liu Lydia Y.ORCID, Carlin BenjaminORCID, Holmes AaronORCID, Oh JieunORCID, Sahrmann JohnORCID, Tao ShuORCID, Eng StefanORCID, Hugh-White RupertORCID, Pashminehazar KiarodORCID, Park Andrew, Beshlikyan ArpiORCID, Jordan MadisonORCID, Wu SelinaORCID, Tian MaoORCID, Arbet JaronORCID, Neilsen BethORCID, Bugh Yuan ZheORCID, Kim GinaORCID, Salmingo JosephORCID, Zhang WenshuORCID, Haas RoniORCID, Anand Aakarsh, Hwang Edward, Neiman-Golden Anna, Steinberg Philippa, Zhao WenyanORCID, Anand Prateek, Tsai Brandon L.ORCID, Boutros Paul C.ORCID
Abstract
AbstractSummaryDNA 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.AvailabilityMetapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is freely available athttps://github.com/uclahs-cds/metapipeline-DNA.
Publisher
Cold Spring Harbor Laboratory
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