Department of Basic and Clinical Neuroscience, King's College London, London, United Kingdom.
Department of Biostatistics and Health Informatics, King's College London, London, United Kingdom.
Bioinformatics. 2023 Apr 3;39(4). doi: 10.1093/bioinformatics/btad152.
The current widespread adoption of next-generation sequencing (NGS) in all branches of basic research 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 software. 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 standard steps of NGS analysis, from quality control of raw data and genome alignment to variant calling, annotation, and generation of reports for the interpretation and prioritization of results; (iii) is highly adaptable as it can be deployed and run via either a graphic user interface for non-bioinformaticians and a command line tool for personal computer usage; (iv) is scalable as it can be executed in parallel as a Snakemake workflow, and; (v) is computationally efficient by minimizing RAM and CPU time requirements.
DNAscan2 is implemented in Python3 and is available at https://github.com/KHP-Informatics/DNAscanv2.
目前，下一代测序（NGS）在基础研究和临床遗传学领域的各个分支中得到了广泛应用，这意味着具有高度变化的信息学技能、计算设施和应用目的的用户需要处理、分析和解释 NGS 数据。在这种情况下，多功能性、可扩展性和用户友好性是 NGS 分析软件的关键特征。我们开发了 DNAscan2，这是一个用于分析 NGS 数据的高度灵活的端到端管道，它 (i) 可用于检测多种变体类型，包括 SNVs、小插入缺失、转座元件、短串联重复序列和其他大型结构变体；(ii) 涵盖 NGS 分析的所有标准步骤，从原始数据的质量控制和基因组比对到变体调用、注释以及为解释和优先化结果生成报告；(iii) 高度适应，因为它可以通过图形用户界面部署和运行，适用于非生物信息学人员，也可以通过命令行工具在个人计算机上使用；(iv) 可扩展性强，因为它可以作为 Snakemake 工作流程并行执行；(v) 通过最小化 RAM 和 CPU 时间需求，计算效率高。
DNAscan2 是用 Python3 实现的，可在 https://github.com/KHP-Informatics/DNAscanv2 上获得。
