The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data. The pipeline is scalable, modular and flexible. Data analysis and transformation steps can be run individually or together in an automated workflow. Users can easily create new reference databases and can select one of three DNA alignment tools, ranging from ultra-fast low-RAM k-mer-based database search to fully exhaustive gapped DNA alignment, to best fit their analysis needs and computational resources. The pipeline includes an implementation of a published method for taxonomy assignment disambiguation with empirical Bayesian redistribution. The software is installable via the conda resource management framework, has plugins for the QIIME2 and QIITA packages and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomics research.

中文翻译：

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SHOGUN：一种用于微生物组定量的模块化，准确和可扩展的框架。

软件管道SHOGUN对短读shot弹枪宏基因组学测序数据的已知分类学和基因丰度进行了分析。管道是可扩展的，模块化的和灵活的。数据分析和转换步骤可以单独运行，也可以在自动化工作流程中一起运行。用户可以轻松创建新的参考数据库，并可以选择三种DNA对齐工具之一，范围从超快速的低RAM k基于mer的数据库搜索，以完全穷尽地对缺口DNA进行比对，以最适合其分析需求和计算资源。该流水线包括已发布方法的实现，该方法用于通过经验贝叶斯再分配进行分类分配消除歧义。该软件可通过conda资源管理框架安装，具有用于QIIME2和QIITA软件包的插件，并且可通过单个命令生成分类法和基因丰度概况表，从而促进了方便和可重复的宏基因组学研究。