PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.
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作者：
Gregor I;Dröge J;Schirmer M;Quince C;McHardy AC
背景资料。元基因组学是一种在原位表征环境微生物群落的方法，它允许对它们的功能和分类进行鉴定，并从未培养的分类群中恢复序列。这通常是通过序列组装和入库的组合来实现的，其中序列被分组到代表底层微生物群落的分类群的“箱”中。对于入库方法来说，分配到低级别的分类库是一个重要的挑战，对于用深度测序技术生成的GB大小的数据集来说，可扩展性也是一个重要的挑战。从深度分枝的门中恢复种库的最佳方法之一是专家训练的PhyloPythiaS程序包，其中人类专家决定要纳入模型的分类群，并直接基于样本中的标记基因来识别“训练”序列。由于所涉及的人工工作，这种方法不能扩展到多个元基因组样本，并且需要大量的专业知识，这是新进入该领域的研究人员所不具备的。结果。我们开发了PhyloPythiaS+，这是我们的PhyloPythia(S)软件的继任者。新的(+)组件执行以前由人类专家完成的工作。PhyloPythiaS+还包括一种新的k-mer计数算法，它将用于分类入库的4-6-mer的同时计数速度加快了100倍，并将软件的总体执行时间减少了三倍。我们的软件允许用廉价的硬件分析GB大小的超基因组，并以全自动的方式以低错误率恢复物种或属级别的箱。将PhyloPythiaS+模型与Megan模型、Taxator-tk模型、Kraken模型和一般的PhyloPythiaS模型进行了比较。结果表明，与其他方法相比，PhyloPythiaS+对来自新环境的样品表现得特别好。可用性。虚拟机中的PhyloPythiaS+可安装在Windows、Unix系统或OS X上：。
Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: .