Patel Y, Zhu C, Yamaguchi TN, Wang NK, Wiltsie N, Gonzalez AE, Winata HK, Zeltser N, Pan Y, Mootor MFE, Sanders T, Kandoth C, Fitz-Gibbon ST, Livingstone J, Liu LY, Carlin B, Holmes A, Oh J, Sahrmann J, Tao S, Eng S, Hugh-White R, Pashminehazar K, Park A, Beshlikyan A, Jordan M, Wu S, Tian M, Arbet J, Neilsen B, Bugh YZ, Kim G, Salmingo J, Zhang W, Haas R, Anand A, Hwang E, Neiman-Golden A, Steinberg P, Zhao W, Anand P, Tsai BL, Boutros PC. Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline.
BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.09.04.611267. [PMID:
39282325 PMCID:
PMC11398472 DOI:
10.1101/2024.09.04.611267]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Summary
DNA sequencing continues to get cheaper and faster. In parallel, algorithmic innovations have allowed inference of a wide range of nuclear, mitochondrial, somatic and evolutionary from DNA sequencing data. To make automated, high-quality DNA sequencing more readily available, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA supports processing raw sequencing reads through alignment, variant detection, quality control and subclonal reconstruction. Each step supports quality-control, data-visualization and multiple algorithms. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subsect, optimize and optimize analyses, including with automated failure-recovery. Metapipeline-DNA enables high-scale, fault-tolerant, comprehensive analysis of genome sequencing.
Availability
Metapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is available at https://github.com/uclahs-cds/metapipeline-DNA.
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