Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
Gigascience. 2013 Mar 13;2(1):3. doi: 10.1186/2047-217X-2-3.
Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.
AXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur. AXIOME also implements features including the PAired-eND Assembler for Illumina sequences (PANDAseq), non-negative matrix factorization (NMF), multi-response permutation procedures (MRPP), exploring and recovering phylogenetic novelty (SSUnique) and indicator species analysis. AXIOME has a companion graphical user interface (GUI) and is designed to be easily extended to facilitate customized research workflows.
AXIOME is an actively developed, open source project written in Vala and available from GitHub (http://neufeld.github.com/axiome) and as a Debian package. Axiometic, a GUI companion tool is also freely available (http://neufeld.github.com/axiometic). Given that data analysis has become an important bottleneck for microbial ecology studies, the development of user-friendly computational tools remains a high priority. AXIOME represents an important step in this direction by automating multi-step bioinformatic analyses and enabling the customization of procedures to suit the diverse research needs of the microbial ecology community.
尽管高通量测序小亚基 rRNA 基因已经彻底改变了我们对微生物生态系统的理解，但这些技术生成的数据深度受益于自动化分析。在这里，我们提出了 AXIOME（微生物生态学的自动化、扩展和集成），这是一个高度灵活和可扩展的管理工具，用于流行的微生物生态学分析软件包，促进了微生物研究中的可重复性和定制化。
AXIOME 简化并管理了 QIIME 和 mothur 中小亚基（SSU）rRNA 标记数据的分析。AXIOME 还实现了一些功能，包括用于 Illumina 序列的配对末端组装器（PANDAseq）、非负矩阵分解（NMF）、多响应置换程序（MRPP）、探索和恢复系统发育新颖性（SSUnique）和指示物种分析。AXIOME 有一个配套的图形用户界面（GUI），旨在易于扩展，以方便定制的研究工作流程。
AXIOME 是一个用 Vala 编写的、活跃开发的开源项目，可从 GitHub（http://neufeld.github.com/axiome）和 Debian 软件包中获得。AXIOMETIC 是一个配套的 GUI 工具，也可以免费获得（http://neufeld.github.com/axiometic）。鉴于数据分析已经成为微生物生态学研究的一个重要瓶颈，开发用户友好的计算工具仍然是一个优先事项。AXIOME 通过自动化多步骤生物信息学分析并使过程定制化以适应微生物生态学社区的各种研究需求，在这方面代表了一个重要的步骤。
