DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for next-generation sequencing data
Marriott Heather 1Dobson Richard J 2Iacoangeli Alfredo 3Kabiljo Renata 4Khleifat Ahmad Al 5Al-Chalabi Ammar6
作者信息
- 1. Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King?ˉs College London||Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King?ˉs College London
- 2. Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King?ˉs College London||NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King?ˉs College London||Institute of Health Informatics, University College London||NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust
- 3. Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King?ˉs College London||Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King?ˉs College London||NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King?ˉs College London
- 4. Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King?ˉs College London
- 5. Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King?ˉs College London
- 6. Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King?ˉs College London||King?ˉs College Hospital
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Abstract
Abstract
The current widespread adoption of next-generation sequencing (NGS) in all branches of basic and clinical genetics fields means that users with highly variable informatics skills, computing facilities and application purposes need to process, analyse, and interpret NGS data. In this landscape, versatility, scalability, and user-friendliness are key characteristics for an NGS analysis tool. We developed DNAscan2, a highly flexible, end-to-end pipeline for the analysis of NGS data, which (i) can be used for the detection of multiple variant types, including SNVs, small indels, transposable elements, short tandem repeats and other large structural variants; (ii) covers all steps of the analysis, from quality control of raw data to the generation of html reports for the interpretation and prioritisation of results; (iii) is highly adaptable and scalable as it can be deployed and run via either a graphic user interface for non-bioinformaticians, a command line tool for personal computer usage, or as a Snakemake workflow that facilitates parallel multi-sample execution for high-performance computing environments; (iv) is computationally efficient by minimising RAM and CPU time requirements.
Availability and ImplementationDNAscan2 is implemented in Python3 and is available to download as a command-line tool and graphical-user interface at https://github.com/KHP-Informatics/DNAscanv2 or a Snakemake workflow at https://github.com/KHP-Informatics/DNAscanv2_snakemake.引用本文复制引用
Marriott Heather,Dobson Richard J,Iacoangeli Alfredo,Kabiljo Renata,Khleifat Ahmad Al,Al-Chalabi Ammar.DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for next-generation sequencing data[EB/OL].(2025-03-28)[2026-04-04].https://www.biorxiv.org/content/10.1101/2022.05.12.491669.学科分类
生物科学研究方法、生物科学研究技术/计算技术、计算机技术/遗传学
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