Morais Daniel, Roesch Luiz F W, Redmile-Gordon Marc, Santos Fausto G, Baldrian Petr, Andreote Fernando D, Pylro Victor S
Institute of Microbiology of the CAS, Prague, Czech Republic.
Centro para Pesquisa Interdisciplinar em Biotecnologia, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil.
PeerJ. 2018 Jul 30;6:e5299. doi: 10.7717/peerj.5299. eCollection 2018.
Recent advances in Next-Generation Sequencing (NGS) make comparative analyses of the composition and diversity of whole microbial communities possible at a far greater depth than ever before. This brings new challenges, such as an increased dependence on computation to process these huge datasets. The demand on system resources usually requires migrating from Windows to Linux-based operating systems and prior familiarity with command-line interfaces. To overcome this barrier, we developed a fully automated and easy-to-install package as well as a complete, easy-to-follow pipeline for microbial metataxonomic analysis operating in the Windows Subsystem for Linux (WSL)-Bioinformatics Through Windows (BTW). BTW combines several open-access tools for processing marker gene data, including 16S rRNA, bringing the user from raw sequencing reads to diversity-related conclusions. It includes data quality filtering, clustering, taxonomic assignment and further statistical analyses, directly in WSL, avoiding the prior need of migrating from Windows to Linux. BTW is expected to boost the use of NGS amplicon data by facilitating rapid access to a set of bioinformatics tools for Windows users. Moreover, several Linux command line tools became more reachable, which will enhance bioinformatics accessibility to a wider range of researchers and practitioners in the life sciences and medicine. BTW is available in GitHub (https://github.com/vpylro/BTW). The package is freely available for noncommercial users.
新一代测序（NGS）技术的最新进展使得对整个微生物群落的组成和多样性进行比较分析成为可能，其深度远超以往。这带来了新的挑战，比如对处理这些庞大数据集的计算依赖性增加。对系统资源的需求通常要求从基于Windows的操作系统迁移到基于Linux的操作系统，并且需要事先熟悉命令行界面。为克服这一障碍，我们开发了一个全自动且易于安装的软件包以及一套完整、易于遵循的流程，用于在适用于Linux的Windows子系统（WSL）——通过Windows进行生物信息学（BTW）中开展微生物元分类分析。BTW整合了多个用于处理标记基因数据（包括16S rRNA）的开放获取工具，可让用户从原始测序读数得出与多样性相关的结论。它直接在WSL中进行数据质量过滤、聚类、分类学归属及进一步的统计分析，避免了事先从Windows迁移到Linux的需要。预计BTW将通过为Windows用户提供一套生物信息学工具，促进NGS扩增子数据的使用。此外，多个Linux命令行工具变得更容易使用，这将提高生物信息学对生命科学和医学领域更广泛的研究人员和从业者的可及性。BTW可在GitHub（https://github.com/vpylro/BTW）上获取。该软件包对非商业用户免费提供。
