VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data.
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data.
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DOI：
10.1186/s40168-014-0066-1
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发表时间：
2015
期刊：
影响因子：
15.5
通讯作者：
Wilmes P
中科院分区：
文献类型：
--
作者：
Laczny CC;Sternal T;Plugaru V;Gawron P;Atashpendar A;Margossian HH;Coronado S;der Maaten Lv;Vlassis N;Wilmes P
由于目前缺乏代表性的分离株基因组序列，宏基因组学在将不同微生物种群与遗传潜力联系起来的能力方面受到限制。不依赖参考的方法，其利用例如用于宏基因组片段聚类（分箱）的固有基因组签名，提供了在不需要先验知识的情况下解析和重建群体水平基因组互补的前景。我们提出了VizBin，一个基于Java™的应用程序，它提供了来自单个样本的宏基因组数据集的高效和直观的独立参考可视化，用于后续的人在环检查和分箱。该方法是基于非线性降维的基因组签名，并利用上级模式识别能力的人类眼睛-大脑系统的聚类识别和划定。我们证明了VizBin的宏基因组序列数据分析的普遍适用性，从两个纤维素分解微生物群落和一个人源性微生物财团的结果。我们的应用程序相比，其他类似的宏基因组可视化和分箱方法的上级性能。VizBin可以从头应用于来自单个样品的宏基因组数据集的可视化和随后的分箱，并且它可以用于自动生成的箱的事后检查和细化。由于其计算效率，它可以在普通的台式机上运行，并在几分钟内分析复杂的宏基因组数据集。该软件实现可在https://claczny.github.io/VizBin上获得，采用BSD许可证（四条款），并在Microsoft Windows™、Apple Mac OS X™（10.7至10.10）和Linux下运行。本文的在线版本（doi：10.1186/s40168-014-0066-1）包含补充材料，可供授权用户使用。
Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge. We present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented. VizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux. The online version of this article (doi:10.1186/s40168-014-0066-1) contains supplementary material, which is available to authorized users.
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影响因子：
56.9
作者：
Venter, JC;Remington, K;Smith, HO
通讯作者：
Smith, HO
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
DOI：
10.1073/pnas.1402564111
发表时间：
2014-04-01
影响因子：
11.1
作者：
Howe, Adina Chuang;Jansson, Janet K.;Brown, C. Titus
通讯作者：
Brown, C. Titus
影响因子：
56.9
作者：
Wrighton, Kelly C.;Thomas, Brian C.;Banfield, Jillian F.
通讯作者：
Banfield, Jillian F.