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Methods ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00999

An integrated pipeline for annotation and visualization of metagenomic contigs

  • 1Department of Geoscience, University of Calgary, Canada

Here we describe MetaErg, a stand-alone 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. 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.

Keywords: Proteomics, Bioinforamtics, gene prediction, functional annotation, Taxonomic assignment, Pathway prediction, visualization, Metagenome assembled genomes (MAGs), gene ontology, abundance, Quantifcation, Binning, Metagenomics

Received: 08 Apr 2019; Accepted: 20 Sep 2019.

Copyright: © 2019 Dong and Strous. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Mrs. Xiaoli Dong, Department of Geoscience, University of Calgary, Calgary, T2N 1N4, Alberta, Canada, xdong@ucalgary.ca