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Analysis of large 16S rRNArRNA Illumina data sets: Impact of singleton read filtering on microbial community description

机译：大16S rrna rRNA Illumina数据集：单例读取过滤对微生物社区描述的影响

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Abstract > Next‐generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S <fc>rRNA</fc> gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of <fc>OTU</fc> predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant <fc>OTU</fc> s, considering them as noise. Although the effect of applying an <fc>OTU</fc> abundance threshold on α‐ and β‐diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering ( <fc>SRF</fc> ) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that <fc>SRF</fc> drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, <fc>SRF</fc> accurately determines the actual community diversity: the differences in α‐ and β‐community diversity obtained with <fc>SRF</fc> and standard procedures are much smaller than the intrinsic variability of technical and biological replicates. </abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> <div class="translation abstracttxt"> <span class="zhankaihshouqi fivelineshidden" id="abstract"> <span>机译：</span><Abstract XMLNS =“http://www.wiley.com/namespaces/wiley”type =“main”xml：id =“men12700-abs-0001”> <标题类型=“main”>抽象</ title> < p>下一代测序技术可访问大量数据，这在基于16S <FC> RRNA </ FC>基因的微生物分集的研究中非常有用。然而，这种大数据集的生产不仅通过技术偏差和测序噪声而损坏，而且还增加了计算时间和光盘空间使用。提高<FC> OTU </ FC>预测的准确性并克服计算，存储和噪声问题，最近的研究和工具建议删除所有单个读取和低丰富的<FC> OTU </ FC> S，将其视为噪音。虽然应用了α-和β-多样性的施加<fc> otu </ fc>丰度阈值的影响已经充分记录，但删除了单一读取的后果已经很差。在这里，我们在Silico模拟数据集中测试单例读取滤波（<FC> SRF </ FC>）对微生物群落组合物的影响以及显示不同级别的多样性和丰度简档的合成和真实社区的测序数据。还使用完整的MISEQ运行评估大数据集的可扩展性。我们表明<FC> SRF </ FC>大大降低了嵌合体内容和计算时间，从几分钟内完成了完整的Miseq的分析。此外，<FC> SRF </ FC>准确地确定了实际的社区多样性：用<FC> SRF </ FC>获得的α-和β-社区多样性的差异远小于技术和技术的内在变异性生物重复。 </ p> </ abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> </div> <div class="record"> <h2 class="all_title" id="enpatent33" >著录项</h2> <ul> <li> <span class="lefttit">来源</span> <div style="width: 86%;vertical-align: text-top;display: inline-block;"> <a href='/journal-foreign-25257/'>《Molecular ecology resources》</a> <b style="margin: 0 2px;">|</b><span>2017年第6期</span><b style="margin: 0 2px;">|</b><span>共11页</span> </div> </li> <li> <div class="author"> <span class="lefttit">作者</span> <p id="fAuthorthree" class="threelineshidden zhankaihshouqi"> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Auer Lucas&option=202" target="_blank" rel="nofollow">Auer Lucas;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Mariadassou Mahendra&option=202" target="_blank" rel="nofollow">Mariadassou Mahendra;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=ODonohue Michael&option=202" target="_blank" rel="nofollow">ODonohue Michael;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Klopp Christophe&option=202" target="_blank" rel="nofollow">Klopp Christophe;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Hernandez‐Raquet Guillermina&option=202" target="_blank" rel="nofollow">Hernandez‐Raquet Guillermina;</a> </p> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zkzz" style="display: none;">展开▼</span> </div> </li> <li> <div style="display: flex;"> <span class="lefttit">作者单位</span> <div style="position: relative;margin-left: 3px;max-width: 639px;"> <div class="threelineshidden zhankaihshouqi" id="fOrgthree"> <p>INSAToulouse Cedex 4 France;</p> <p>MaIAGEJouy‐en‐Josas France;</p> <p>INSAToulouse Cedex 4 France;</p> <p>INRAToulouse France;</p> <p>INSAToulouse Cedex 4 France;</p> </div> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zhdw" style="display: none;">展开▼</span> </div> </div> </li> <li > <span class="lefttit">收录信息</span> <span style="width: 86%;vertical-align: text-top;display: inline-block;"></span> </li> <li> <span class="lefttit">原文格式</span> <span>PDF</span> </li> <li> <span class="lefttit">正文语种</span> <span>eng</span> </li> <li> <span class="lefttit">中图分类</span> <span><a href="https://www.zhangqiaokeyan.com/clc/179.html" title="分子生物学">分子生物学;</a></span> </li> <li class="antistop"> <span class="lefttit">关键词</span> <p style="width: 86%;vertical-align: text-top;"> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=16Sr RNA&option=203" rel="nofollow">16Sr RNA;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Illumina&option=203" rel="nofollow">Illumina;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=metabarcoding&option=203" rel="nofollow">metabarcoding;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=microbial diversity&option=203" rel="nofollow">microbial diversity;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=singleton filtering&option=203" rel="nofollow">singleton filtering;</a> </p> <div class="translation"> 机译：16SR RNA;Illumina;Metabarcoding;微生物多样性;单身滤波; 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