ASA³P Software & Database volume

ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates. https://github.com/oschwengers/asap ASA³P is a fully automatic, locally executable and scalable assembly, annotation and higher-level analysis pipeline creating results in standard bioinformatics file formats as well as sophisticated HTML5 documents. Its main purpose is the automatic processing of NGS WGS data of multiple closely related isolates, thus transforming raw reads into assembled and annotated genomes and finally gathering as much information on every single bacterial genome as possible. Per-isolate analyses are complemented by comparative insights. Therefore, the pipeline incorporates many best-in-class open source bioinformatics tools and thus minimizes the burden of ever-repeating tasks. Envisaged as a preprocessing tool it provides comprehensive insights as well as a general overview and comparison of analysed genomes along with all necessary result files for subsequent deeper analyses. All results are presented via modern HTML5 documents comprising interactive visualizations. Schwengers et al, 2020 PLOS Comp Bio DOI:10.1371/journal.pcbi.1007134ASA³P是一款面向近缘细菌分离株的自动化、高可扩展性基因组组装、注释及高阶分析流程。https://github.com/oschwengers/asap ASA³P为全自动化、可本地执行且具备良好可扩展性的组装、注释与高阶分析流程，可生成标准生物信息学文件格式以及精致的HTML5格式分析文档。其核心用途为自动化处理多株近缘分离株的下一代测序（Next-Generation Sequencing, NGS）与全基因组测序（Whole Genome Sequencing, WGS）原始数据，可将原始测序读段转化为完成组装与注释的基因组，并最终尽可能获取每一株细菌基因组的完整信息。单株分离株的分析结果还会辅以比较基因组学层面的洞察。为此，该流程整合了多款业界领先的开源生物信息学工具，从而极大降低了重复执行任务带来的工作负担。作为一款预处理工具，它不仅可提供全面的分析洞察，还能为已分析基因组提供通用概览与对比信息，并附带所有用于后续深度分析的必要结果文件。所有分析结果均通过搭载交互式可视化功能的现代化HTML5文档进行展示。Schwengers 等，2020，《公共科学图书馆·计算生物学》（PLOS Computational Biology），DOI:10.1371/journal.pcbi.1007134