An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
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DOI：
10.3389/fgene.2019.00999
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发表时间：
2019-10-15
影响因子：
3.7
通讯作者：
Strous, Marc
中科院分区：
文献类型：
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作者：
Dong, Xiaoli;Strous, Marc
在这里，我们描述MetaErg，一个独立的和完全自动化的宏基因组和元蛋白质组注释管道。宏基因组的注释是具有挑战性的。首先，宏基因组包含来自所有生命领域的许多生物体的序列数据。第二，这些基因中有许多来自未被充分研究的谱系，编码与实验验证的参考基因相似性低的基因。第三，组装和分箱并不完美，有时会导致人为的杂交重叠群或基因组。为了解决这些挑战，MetaErg提供了完整宏基因组和单个宏基因组组装基因组（MAG）的注释结果的图形摘要。它对每个基因进行全面的注释，包括分类学分类，尽管与参考基因的相似性较低，但仍能进行功能推断，以及检测潜在的组装或分箱伪影。当提供元蛋白质组信息时，它分别使用测序覆盖率和蛋白质组光谱计数来可视化基因和途径活性。对于可视化，MetaErg提供了一个HTML界面，将所有注释结果放在一起，并生成可排序和可搜索的表格，可折叠的树和其他图形表示，从而实现复杂数据的直观导航。MetaErg，用Perl，HTML和JavaScript实现，是一个完全开源的应用程序，在https://github.com/xiaoli-dong/metaerg上根据学术自由许可证分发。MetaErg也可以在https://hub.docker.com/r/xiaolidong/ docker-metaerg上作为docker镜像获得。
Here, we describe MetaErg, a standalone and fully automated metagenome and metaproteome annotation pipeline. Annotation of metagenomes is challenging. First, metagenomes contain sequence data of many organisms from all domains of life. Second, many of these are from understudied lineages, encoding genes with low similarity to experimentally validated reference genes. Third, assembly and binning are not perfect, sometimes resulting in artifactual hybrid contigs or genomes. To address these challenges, MetaErg provides graphical summaries of annotation outcomes, both for the complete metagenome and for individual metagenome-assembled genomes (MAGs). It performs a comprehensive annotation of each gene, including taxonomic classification, enabling functional inferences despite low similarity to reference genes, as well as detection of potential assembly or binning artifacts. When provided with metaproteome information, it visualizes gene and pathway activity using sequencing coverage and proteomic spectral counts, respectively. For visualization, MetaErg provides an HTML interface, bringing all annotation results together, and producing sortable and searchable tables, collapsible trees, and other graphic representations enabling intuitive navigation of complex data. MetaErg, implemented in Perl, HTML, and JavaScript, is a fully open source application, distributed under Academic Free License at https://github.com/xiaoli-dong/metaerg. MetaErg is also available as a docker image at https://hub.docker.com/r/xiaolidong/ docker-metaerg.