Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package
Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package
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DOI：
10.1007/978-1-4939-6685-1_9
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发表时间：
2017-01-01
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影响因子：
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通讯作者：
Tannock, Gerald W.
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文献类型：
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作者：
Lawley, Blair;Tannock, Gerald W.
近年来，微生物生态学的研究经历了范式转变，分子和生物信息学工具的快速发展使具有广泛兴趣和背景的研究人员能够获得社区分析方法。虽然这些进展无疑导致了对许多系统令人兴奋的新理解，但可用的一系列协议和特定方法的特性可能导致混淆，或者在最坏的情况下，对结果的错误解释。在这里，我们描述了一个工作流程，从原始的16S rRNA基因扩增子序列数据，在Illumina MiSeq仪器上生成，微生物群落分类概况和基本的多样性措施。该工作流程可以适应主要序列平台的输入，并使用可以在一系列操作系统上实现的免费开源软件。
The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures. The workflow can be adapted to input from major sequence platforms and uses freely available open source software that can be implemented on a range of operating systems.